Starting phenix.real_space_refine on Thu Dec 7 17:26:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qig_13989/12_2023/7qig_13989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qig_13989/12_2023/7qig_13989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qig_13989/12_2023/7qig_13989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qig_13989/12_2023/7qig_13989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qig_13989/12_2023/7qig_13989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qig_13989/12_2023/7qig_13989.pdb" } resolution = 2.7 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 2007 2.51 5 N 570 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 146": "OD1" <-> "OD2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 166": "OD1" <-> "OD2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 220": "OE1" <-> "OE2" 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: 3213 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1071 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1071 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "C" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1071 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Time building chain proxies: 2.20, per 1000 atoms: 0.68 Number of scatterers: 3213 At special positions: 0 Unit cell: (90.695, 124.839, 39.479, 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 609 8.00 N 570 7.00 C 2007 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 B 178 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 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: 1.13 Conformation dependent library (CDL) restraints added in 591.7 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 738 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 71.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.310A pdb=" N HIS A 95 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TRP B 98 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN A 97 " --> pdb=" O TRP B 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 115 removed outlier: 6.880A pdb=" N VAL B 111 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 112 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B 113 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 111 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA C 112 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 113 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 120 through 121 removed outlier: 6.584A pdb=" N VAL A 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 134 removed outlier: 6.324A pdb=" N TYR A 127 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY B 130 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N LEU A 129 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA B 132 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N SER A 131 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N SER B 134 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N MET A 133 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER C 131 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA A 132 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N MET C 133 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER A 134 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.350A pdb=" N ILE A 138 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 146 removed outlier: 6.237A pdb=" N ASN A 142 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLU B 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP A 144 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 150 removed outlier: 6.418A pdb=" N TYR A 149 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 155 removed outlier: 6.734A pdb=" N TYR A 154 " --> pdb=" O ARG C 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.505A pdb=" N GLN A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR B 162 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A 161 " --> pdb=" O TYR B 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 166 through 172 removed outlier: 7.025A pdb=" N GLN B 171 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN A 172 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN A 167 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN C 170 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N SER A 169 " --> pdb=" O ASN C 170 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN C 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N GLN A 171 " --> pdb=" O ASN C 172 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 191 removed outlier: 8.937A pdb=" N VAL A 175 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS B 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASP A 177 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N ASN B 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 179 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 182 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 181 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS B 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 183 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS B 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 185 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL B 188 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 187 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 190 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 189 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY B 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N LYS A 193 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N ASN B 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLU A 195 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 197 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 200 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU A 199 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N VAL B 202 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 201 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N MET B 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 203 " --> pdb=" O MET B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 191 removed outlier: 8.937A pdb=" N VAL A 175 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N CYS B 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASP A 177 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 9.686A pdb=" N ASN B 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL A 179 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N THR B 182 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 181 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS B 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 183 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS B 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN A 185 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL B 188 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR A 187 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 190 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 189 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP C 177 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 178 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 179 " --> pdb=" O CYS A 178 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN A 180 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS C 193 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A 194 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU C 195 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 211 through 219 removed outlier: 7.061A pdb=" N CYS B 213 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 214 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 215 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLN A 211 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL C 214 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N CYS A 213 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N GLN C 216 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR A 215 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN C 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR A 217 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 224 removed outlier: 6.598A pdb=" N ALA A 223 " --> pdb=" O TYR B 224 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 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: 0.72 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1065 1.34 - 1.46: 707 1.46 - 1.58: 1474 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 3294 Sorted by residual: bond pdb=" C LYS B 103 " pdb=" O LYS B 103 " ideal model delta sigma weight residual 1.233 1.224 0.009 4.80e-03 4.34e+04 3.61e+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 2.95e+00 bond pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CB ARG B 207 " pdb=" CG ARG B 207 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.43e-01 ... (remaining 3289 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.65: 74 105.65 - 112.77: 1658 112.77 - 119.88: 1047 119.88 - 126.99: 1636 126.99 - 134.10: 46 Bond angle restraints: 4461 Sorted by residual: angle pdb=" C TYR C 162 " pdb=" N ARG C 163 " pdb=" CA ARG C 163 " ideal model delta sigma weight residual 122.59 117.40 5.19 1.11e+00 8.12e-01 2.19e+01 angle pdb=" N ARG A 163 " pdb=" CA ARG A 163 " pdb=" C ARG A 163 " ideal model delta sigma weight residual 109.30 113.66 -4.36 1.49e+00 4.50e-01 8.57e+00 angle pdb=" N ARG C 163 " pdb=" CA ARG C 163 " pdb=" C ARG C 163 " ideal model delta sigma weight residual 109.30 112.74 -3.44 1.49e+00 4.50e-01 5.33e+00 angle pdb=" N GLY C 123 " pdb=" CA GLY C 123 " pdb=" C GLY C 123 " ideal model delta sigma weight residual 113.18 118.41 -5.23 2.37e+00 1.78e-01 4.87e+00 angle pdb=" C GLU A 195 " pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " ideal model delta sigma weight residual 112.00 108.15 3.85 1.79e+00 3.12e-01 4.63e+00 ... (remaining 4456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1805 17.96 - 35.93: 102 35.93 - 53.89: 37 53.89 - 71.86: 9 71.86 - 89.82: 6 Dihedral angle restraints: 1959 sinusoidal: 795 harmonic: 1164 Sorted by residual: dihedral pdb=" CA CYS B 178 " pdb=" C CYS B 178 " pdb=" N VAL B 179 " pdb=" CA VAL B 179 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET C 204 " pdb=" C MET C 204 " pdb=" N MET C 205 " pdb=" CA MET C 205 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA CYS A 178 " pdb=" C CYS A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 238 0.033 - 0.066: 149 0.066 - 0.098: 33 0.098 - 0.131: 22 0.131 - 0.163: 14 Chirality restraints: 456 Sorted by residual: 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 2.60 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA VAL C 175 " pdb=" N VAL C 175 " pdb=" C VAL C 175 " pdb=" CB VAL C 175 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL A 175 " pdb=" N VAL A 175 " pdb=" C VAL A 175 " pdb=" CB VAL A 175 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 453 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 207 " 0.277 9.50e-02 1.11e+02 1.24e-01 9.44e+00 pdb=" NE ARG B 207 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 207 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 207 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 207 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 163 " -0.194 9.50e-02 1.11e+02 8.71e-02 4.86e+00 pdb=" NE ARG C 163 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 163 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 163 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 163 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 146 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CG ASP A 146 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 146 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 146 " 0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 37 2.69 - 3.24: 2767 3.24 - 3.80: 5117 3.80 - 4.35: 6629 4.35 - 4.90: 11919 Nonbonded interactions: 26469 Sorted by model distance: nonbonded pdb=" NZ LYS B 193 " pdb=" OE2 GLU B 195 " model vdw 2.138 2.520 nonbonded pdb=" O THR B 191 " pdb=" OG1 THR B 191 " model vdw 2.483 2.440 nonbonded pdb=" OG1 THR A 215 " pdb=" O THR B 215 " model vdw 2.498 2.440 nonbonded pdb=" O HIS B 176 " pdb=" OD1 ASP B 177 " model vdw 2.501 3.040 nonbonded pdb=" O HIS A 176 " pdb=" OD1 ASP A 177 " model vdw 2.501 3.040 ... (remaining 26464 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: 2.320 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: 11.050 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.110 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.005 0.033 3294 Z= 0.317 Angle : 0.695 5.229 4461 Z= 0.401 Chirality : 0.051 0.163 456 Planarity : 0.007 0.124 585 Dihedral : 14.668 89.822 1212 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % 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: -4.18 (0.28), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.21), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 98 HIS 0.004 0.001 HIS C 139 PHE 0.021 0.004 PHE B 140 TYR 0.025 0.003 TYR A 149 ARG 0.008 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.386 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 86 average time/residue: 1.7265 time to fit residues: 151.1952 Evaluate side-chains 74 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.9131 time to fit residues: 1.4353 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3294 Z= 0.242 Angle : 0.658 5.522 4461 Z= 0.367 Chirality : 0.050 0.146 456 Planarity : 0.003 0.029 585 Dihedral : 6.191 18.280 444 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.90 % Allowed : 10.72 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 98 HIS 0.003 0.001 HIS A 139 PHE 0.026 0.005 PHE A 140 TYR 0.018 0.002 TYR A 148 ARG 0.004 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.403 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 78 average time/residue: 1.9052 time to fit residues: 151.3168 Evaluate side-chains 74 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0399 time to fit residues: 0.6846 ------------------------------------------------------------------------------- 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: 0.5980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.0050 chunk 26 optimal weight: 0.5980 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3294 Z= 0.273 Angle : 0.663 5.936 4461 Z= 0.367 Chirality : 0.049 0.144 456 Planarity : 0.004 0.024 585 Dihedral : 6.089 18.537 444 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.77 % Allowed : 10.14 % Favored : 86.09 % 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: -4.15 (0.29), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.22), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 98 HIS 0.004 0.001 HIS C 139 PHE 0.026 0.005 PHE A 140 TYR 0.017 0.002 TYR C 149 ARG 0.007 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.391 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 79 average time/residue: 1.7248 time to fit residues: 138.7992 Evaluate side-chains 77 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.9453 time to fit residues: 3.3836 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8334 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3294 Z= 0.278 Angle : 0.659 5.948 4461 Z= 0.363 Chirality : 0.049 0.143 456 Planarity : 0.004 0.026 585 Dihedral : 6.033 18.940 444 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.61 % Allowed : 11.88 % Favored : 85.51 % 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: -4.17 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.23), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 98 HIS 0.004 0.001 HIS C 139 PHE 0.025 0.005 PHE A 140 TYR 0.017 0.002 TYR C 149 ARG 0.002 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.409 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 77 average time/residue: 1.8069 time to fit residues: 141.6636 Evaluate side-chains 76 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4777 time to fit residues: 1.4244 ------------------------------------------------------------------------------- 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: 0.0980 chunk 15 optimal weight: 0.0060 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3294 Z= 0.153 Angle : 0.580 4.834 4461 Z= 0.320 Chirality : 0.047 0.140 456 Planarity : 0.003 0.031 585 Dihedral : 5.728 18.564 444 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.32 % Allowed : 12.75 % Favored : 84.93 % 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: -4.21 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.23), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 98 HIS 0.002 0.001 HIS C 139 PHE 0.024 0.004 PHE A 140 TYR 0.014 0.001 TYR A 148 ARG 0.004 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.404 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 77 average time/residue: 1.8343 time to fit residues: 143.8932 Evaluate side-chains 79 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4375 time to fit residues: 2.0108 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3294 Z= 0.395 Angle : 0.721 6.368 4461 Z= 0.395 Chirality : 0.050 0.150 456 Planarity : 0.005 0.045 585 Dihedral : 6.129 18.971 444 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.61 % Allowed : 13.91 % Favored : 83.48 % 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: -4.16 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.23), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 98 HIS 0.006 0.002 HIS C 139 PHE 0.026 0.006 PHE A 174 TYR 0.018 0.002 TYR A 148 ARG 0.006 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.352 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 1.7693 time to fit residues: 138.7362 Evaluate side-chains 77 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0362 time to fit residues: 0.5734 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3294 Z= 0.214 Angle : 0.619 5.372 4461 Z= 0.341 Chirality : 0.048 0.134 456 Planarity : 0.004 0.038 585 Dihedral : 5.900 18.616 444 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 3.77 % Allowed : 14.20 % Favored : 82.03 % 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: -4.19 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.23), residues: 390 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 0.024 0.005 PHE A 140 TYR 0.015 0.002 TYR A 148 ARG 0.005 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.394 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 76 average time/residue: 1.7437 time to fit residues: 135.0329 Evaluate side-chains 76 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 1.1601 time to fit residues: 4.0718 ------------------------------------------------------------------------------- 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: 0.6980 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 27 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3294 Z= 0.185 Angle : 0.592 4.964 4461 Z= 0.326 Chirality : 0.047 0.132 456 Planarity : 0.003 0.032 585 Dihedral : 5.748 18.637 444 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.61 % Allowed : 14.78 % Favored : 82.61 % 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: -4.18 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.23), residues: 390 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 0.023 0.005 PHE A 140 TYR 0.019 0.002 TYR B 149 ARG 0.004 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.354 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 77 average time/residue: 1.7377 time to fit residues: 136.3145 Evaluate side-chains 76 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5191 ------------------------------------------------------------------------------- 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: 0.3980 chunk 34 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.8275 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3294 Z= 0.167 Angle : 0.578 5.314 4461 Z= 0.318 Chirality : 0.047 0.132 456 Planarity : 0.003 0.027 585 Dihedral : 5.629 18.529 444 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 2.03 % Allowed : 15.94 % Favored : 82.03 % 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: -4.18 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.23), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 98 HIS 0.002 0.001 HIS C 139 PHE 0.022 0.004 PHE A 140 TYR 0.018 0.001 TYR B 149 ARG 0.004 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.400 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 80 average time/residue: 1.6357 time to fit residues: 133.4521 Evaluate side-chains 78 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.7962 time to fit residues: 2.1532 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 0.0570 chunk 24 optimal weight: 0.0170 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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: 0.8265 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3294 Z= 0.157 Angle : 0.574 5.362 4461 Z= 0.316 Chirality : 0.047 0.132 456 Planarity : 0.003 0.028 585 Dihedral : 5.548 18.499 444 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.45 % Allowed : 17.68 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.23), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 98 HIS 0.002 0.001 HIS C 139 PHE 0.022 0.004 PHE A 140 TYR 0.019 0.001 TYR B 149 ARG 0.003 0.000 ARG C 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.376 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 1.7649 time to fit residues: 140.2201 Evaluate side-chains 77 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.338 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.9153 time to fit residues: 1.3878 ------------------------------------------------------------------------------- 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: 0.7980 chunk 27 optimal weight: 0.0010 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.114094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103284 restraints weight = 4338.234| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.41 r_work: 0.3386 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3294 Z= 0.201 Angle : 0.601 5.430 4461 Z= 0.330 Chirality : 0.047 0.132 456 Planarity : 0.003 0.030 585 Dihedral : 5.668 18.159 444 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.87 % Allowed : 18.26 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.30), residues: 390 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.23), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.003 0.001 HIS C 139 PHE 0.022 0.005 PHE A 140 TYR 0.020 0.002 TYR B 149 ARG 0.004 0.000 ARG C 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.86 seconds wall clock time: 48 minutes 25.68 seconds (2905.68 seconds total)