Starting phenix.real_space_refine on Thu Dec 7 18:00:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/12_2023/8a00_15043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/12_2023/8a00_15043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/12_2023/8a00_15043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/12_2023/8a00_15043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/12_2023/8a00_15043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a00_15043/12_2023/8a00_15043.pdb" } resolution = 2.6 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= 0.001 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 27 5.16 5 C 2061 2.51 5 N 600 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B ASP 177": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3315 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1105 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "C" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1105 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "B" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1105 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Time building chain proxies: 2.41, per 1000 atoms: 0.73 Number of scatterers: 3315 At special positions: 0 Unit cell: (108.468, 113.436, 35.604, 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 27 16.00 O 627 8.00 N 600 7.00 C 2061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.23 Conformation dependent library (CDL) restraints added in 580.9 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 64.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 95 through 99 removed outlier: 6.403A pdb=" N HIS A 95 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N TRP B 98 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN A 97 " --> pdb=" O TRP B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 106 through 111 removed outlier: 6.745A pdb=" N VAL A 111 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 106 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LYS B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 108 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N VAL B 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N HIS A 110 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 114 through 116 removed outlier: 6.557A pdb=" N ALA A 115 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.369A pdb=" N VAL A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 134 removed outlier: 6.413A pdb=" N ALA A 132 " --> pdb=" O MET B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 137 through 144 Processing sheet with id=AA7, first strand: chain 'C' and resid 149 through 150 removed outlier: 6.332A pdb=" N TYR A 149 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 154 through 155 removed outlier: 6.717A pdb=" N TYR A 154 " --> pdb=" O ARG C 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 162 removed outlier: 6.364A pdb=" N ASN A 158 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N TYR C 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 160 " --> pdb=" O TYR C 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 179 removed outlier: 6.058A pdb=" N GLN A 167 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN C 170 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER A 169 " --> pdb=" O ASN C 170 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ASN C 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN A 171 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE C 174 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASN A 173 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 9.936A pdb=" N HIS C 176 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL A 175 " --> pdb=" O HIS C 176 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N CYS C 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP A 177 " --> pdb=" O CYS C 178 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLY C 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 193 " --> pdb=" O GLY C 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 182 through 191 removed outlier: 7.622A pdb=" N ILE C 183 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 182 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLN C 185 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS A 184 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N THR C 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS A 186 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR C 189 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 188 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR C 191 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 190 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE A 174 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 175 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N HIS A 176 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 181 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A 182 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE B 183 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 184 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLN B 185 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS A 186 " --> pdb=" O GLN B 185 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR B 187 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 188 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR B 189 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR A 190 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 191 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR A 192 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 198 through 206 removed outlier: 6.144A pdb=" N THR A 198 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP C 201 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR A 200 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS C 203 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 202 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N MET C 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET A 204 " --> pdb=" O MET C 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 211 through 226 removed outlier: 9.569A pdb=" N GLN A 211 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL C 214 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS A 213 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLN C 216 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 215 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLN C 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A 217 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLU C 220 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LYS A 219 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 10.343A pdb=" N GLN C 222 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N SER A 221 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 9.673A pdb=" N TYR C 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 223 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASP C 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 225 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N CYS B 213 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 214 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU A 220 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 221 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN A 222 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 223 " --> pdb=" O GLN A 222 " (cutoff:3.500A) 65 hydrogen bonds defined for protein. 195 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: 0.88 Time building geometry restraints manager: 1.37 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: 1113 1.34 - 1.46: 741 1.46 - 1.57: 1494 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 3396 Sorted by residual: bond pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" CA ASN A 173 " pdb=" C ASN A 173 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.99e-01 bond pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta sigma weight residual 1.459 1.469 -0.010 1.28e-02 6.10e+03 6.33e-01 ... (remaining 3391 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 98 106.53 - 113.41: 1760 113.41 - 120.29: 1170 120.29 - 127.16: 1524 127.16 - 134.04: 41 Bond angle restraints: 4593 Sorted by residual: angle pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" N PHE A 174 " ideal model delta sigma weight residual 114.17 117.40 -3.23 1.45e+00 4.76e-01 4.96e+00 angle pdb=" CA PRO A 104 " pdb=" C PRO A 104 " pdb=" O PRO A 104 " ideal model delta sigma weight residual 123.16 120.17 2.99 1.49e+00 4.50e-01 4.03e+00 angle pdb=" N ALA C 117 " pdb=" CA ALA C 117 " pdb=" C ALA C 117 " ideal model delta sigma weight residual 108.19 110.71 -2.52 1.29e+00 6.01e-01 3.81e+00 angle pdb=" N ALA A 117 " pdb=" CA ALA A 117 " pdb=" C ALA A 117 " ideal model delta sigma weight residual 108.19 110.60 -2.41 1.29e+00 6.01e-01 3.48e+00 angle pdb=" C PRO C 164 " pdb=" N VAL C 165 " pdb=" CA VAL C 165 " ideal model delta sigma weight residual 122.97 121.15 1.82 9.80e-01 1.04e+00 3.43e+00 ... (remaining 4588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1843 17.94 - 35.88: 138 35.88 - 53.82: 33 53.82 - 71.75: 3 71.75 - 89.69: 8 Dihedral angle restraints: 2025 sinusoidal: 831 harmonic: 1194 Sorted by residual: dihedral pdb=" CB CYS B 178 " pdb=" SG CYS B 178 " pdb=" SG CYS B 213 " pdb=" CB CYS B 213 " ideal model delta sinusoidal sigma weight residual -86.00 -131.14 45.14 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS A 178 " pdb=" SG CYS A 178 " pdb=" SG CYS A 213 " pdb=" CB CYS A 213 " ideal model delta sinusoidal sigma weight residual -86.00 -129.93 43.93 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CB CYS C 178 " pdb=" SG CYS C 178 " pdb=" SG CYS C 213 " pdb=" CB CYS C 213 " ideal model delta sinusoidal sigma weight residual -86.00 -118.68 32.68 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 2022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 253 0.032 - 0.064: 148 0.064 - 0.096: 34 0.096 - 0.128: 25 0.128 - 0.160: 5 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA ILE C 183 " pdb=" N ILE C 183 " pdb=" C ILE C 183 " pdb=" CB ILE C 183 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ILE A 183 " pdb=" N ILE A 183 " pdb=" C ILE A 183 " pdb=" CB ILE A 183 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE B 183 " pdb=" N ILE B 183 " pdb=" C ILE B 183 " pdb=" CB ILE B 183 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 462 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 103 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO C 104 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 103 " -0.018 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 104 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 176 " -0.005 2.00e-02 2.50e+03 9.93e-03 9.86e-01 pdb=" C HIS A 176 " 0.017 2.00e-02 2.50e+03 pdb=" O HIS A 176 " -0.006 2.00e-02 2.50e+03 pdb=" N ASP A 177 " -0.006 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 930 2.84 - 3.35: 2665 3.35 - 3.87: 5785 3.87 - 4.38: 6446 4.38 - 4.90: 11760 Nonbonded interactions: 27586 Sorted by model distance: nonbonded pdb=" O ALA A 112 " pdb=" OG SER B 134 " model vdw 2.321 2.440 nonbonded pdb=" NH2 ARG A 135 " pdb=" OE1 GLU B 151 " model vdw 2.341 2.520 nonbonded pdb=" OG SER A 134 " pdb=" O ALA C 112 " model vdw 2.356 2.440 nonbonded pdb=" O TRP A 98 " pdb=" ND2 ASN A 142 " model vdw 2.413 2.520 nonbonded pdb=" O TRP C 98 " pdb=" ND2 ASN C 142 " model vdw 2.485 2.520 ... (remaining 27581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 4.510 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: 21.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.200 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:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.002 0.033 3396 Z= 0.157 Angle : 0.581 5.421 4593 Z= 0.343 Chirality : 0.047 0.160 465 Planarity : 0.003 0.037 606 Dihedral : 14.424 89.691 1260 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % 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: -3.74 (0.29), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.22), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 98 HIS 0.003 0.001 HIS C 139 PHE 0.006 0.001 PHE A 174 TYR 0.014 0.001 TYR A 149 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.477 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 1.7242 time to fit residues: 139.1503 Evaluate side-chains 73 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN C 196 ASN B 110 HIS B 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3396 Z= 0.300 Angle : 0.663 5.489 4593 Z= 0.371 Chirality : 0.048 0.158 465 Planarity : 0.003 0.027 606 Dihedral : 5.337 14.723 462 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.41 % Allowed : 7.34 % Favored : 91.24 % 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: -3.72 (0.29), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.22), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.012 0.002 PHE A 197 TYR 0.019 0.002 TYR B 148 ARG 0.003 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.397 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 76 average time/residue: 1.7776 time to fit residues: 137.7044 Evaluate side-chains 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3396 Z= 0.270 Angle : 0.636 5.255 4593 Z= 0.357 Chirality : 0.048 0.157 465 Planarity : 0.003 0.023 606 Dihedral : 5.271 14.371 462 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.72 % Favored : 92.79 % Rotamer: Outliers : 1.98 % Allowed : 9.04 % Favored : 88.98 % 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: -3.79 (0.29), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.22), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.012 0.002 PHE A 197 TYR 0.018 0.002 TYR B 148 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 0.464 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 1.8240 time to fit residues: 144.9806 Evaluate side-chains 75 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3396 Z= 0.252 Angle : 0.627 5.246 4593 Z= 0.352 Chirality : 0.047 0.157 465 Planarity : 0.003 0.023 606 Dihedral : 5.198 14.206 462 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.21 % Favored : 92.29 % Rotamer: Outliers : 1.41 % Allowed : 12.43 % Favored : 86.16 % 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: -3.79 (0.29), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.22), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.012 0.002 PHE A 197 TYR 0.018 0.002 TYR B 148 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.381 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 1.6756 time to fit residues: 128.2996 Evaluate side-chains 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.6585 time to fit residues: 2.2051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3396 Z= 0.275 Angle : 0.636 5.179 4593 Z= 0.359 Chirality : 0.048 0.158 465 Planarity : 0.003 0.021 606 Dihedral : 5.241 16.019 462 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.22 % Favored : 93.03 % Rotamer: Outliers : 1.69 % Allowed : 12.99 % Favored : 85.31 % 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: -3.81 (0.29), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.22), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.012 0.002 PHE A 197 TYR 0.018 0.002 TYR B 148 ARG 0.006 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.382 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 76 average time/residue: 1.7236 time to fit residues: 133.5654 Evaluate side-chains 75 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.5590 time to fit residues: 2.1130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3396 Z= 0.228 Angle : 0.611 4.992 4593 Z= 0.343 Chirality : 0.047 0.155 465 Planarity : 0.003 0.027 606 Dihedral : 5.119 14.116 462 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.72 % Favored : 92.54 % Rotamer: Outliers : 1.13 % Allowed : 14.41 % Favored : 84.46 % 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: -3.77 (0.29), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.011 0.002 PHE A 197 TYR 0.017 0.002 TYR B 148 ARG 0.008 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.328 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 72 average time/residue: 1.7974 time to fit residues: 131.8950 Evaluate side-chains 72 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.0040 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3396 Z= 0.178 Angle : 0.599 7.673 4593 Z= 0.334 Chirality : 0.046 0.153 465 Planarity : 0.003 0.026 606 Dihedral : 5.036 15.141 462 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.47 % Favored : 92.79 % Rotamer: Outliers : 1.13 % Allowed : 14.12 % Favored : 84.75 % 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: -3.76 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.010 0.002 PHE A 197 TYR 0.016 0.002 TYR A 148 ARG 0.007 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.387 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 1.7015 time to fit residues: 126.7312 Evaluate side-chains 70 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3396 Z= 0.198 Angle : 0.594 5.452 4593 Z= 0.333 Chirality : 0.047 0.155 465 Planarity : 0.003 0.035 606 Dihedral : 5.020 15.094 462 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.47 % Favored : 92.79 % Rotamer: Outliers : 1.69 % Allowed : 14.12 % Favored : 84.18 % 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: -3.77 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.010 0.002 PHE A 197 TYR 0.016 0.002 TYR B 148 ARG 0.007 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.468 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 70 average time/residue: 1.6936 time to fit residues: 121.0941 Evaluate side-chains 71 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.3870 time to fit residues: 1.9342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3396 Z= 0.259 Angle : 0.616 4.768 4593 Z= 0.347 Chirality : 0.047 0.158 465 Planarity : 0.003 0.020 606 Dihedral : 5.107 14.166 462 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.97 % Favored : 92.29 % Rotamer: Outliers : 1.13 % Allowed : 15.54 % Favored : 83.33 % 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: -3.75 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 98 HIS 0.005 0.001 HIS B 139 PHE 0.013 0.003 PHE A 140 TYR 0.017 0.002 TYR B 148 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.389 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 1.6227 time to fit residues: 125.8694 Evaluate side-chains 78 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.9912 time to fit residues: 1.5242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3396 Z= 0.209 Angle : 0.592 4.679 4593 Z= 0.332 Chirality : 0.047 0.154 465 Planarity : 0.003 0.019 606 Dihedral : 5.064 15.710 462 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.97 % Favored : 92.29 % Rotamer: Outliers : 0.85 % Allowed : 15.82 % Favored : 83.33 % 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: -3.73 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 98 HIS 0.004 0.001 HIS B 139 PHE 0.011 0.002 PHE A 140 TYR 0.016 0.002 TYR A 148 ARG 0.006 0.000 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.422 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 74 average time/residue: 1.7057 time to fit residues: 128.9599 Evaluate side-chains 73 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.131165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.115066 restraints weight = 3619.157| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.47 r_work: 0.3549 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3396 Z= 0.266 Angle : 0.630 5.615 4593 Z= 0.354 Chirality : 0.048 0.158 465 Planarity : 0.003 0.024 606 Dihedral : 5.185 16.041 462 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.46 % Favored : 91.79 % Rotamer: Outliers : 1.13 % Allowed : 15.54 % Favored : 83.33 % 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: -3.73 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 98 HIS 0.005 0.001 HIS C 176 PHE 0.014 0.003 PHE A 140 TYR 0.017 0.002 TYR B 148 ARG 0.007 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.67 seconds wall clock time: 49 minutes 33.10 seconds (2973.10 seconds total)