Starting phenix.real_space_refine on Sat Apr 6 00:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fja_29220/04_2024/8fja_29220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fja_29220/04_2024/8fja_29220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fja_29220/04_2024/8fja_29220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fja_29220/04_2024/8fja_29220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fja_29220/04_2024/8fja_29220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fja_29220/04_2024/8fja_29220.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 4024 2.51 5 N 1117 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 73": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6419 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1645 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 214, 1645 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1620 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2237 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 262} Chain: "B" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Time building chain proxies: 4.09, per 1000 atoms: 0.64 Number of scatterers: 6419 At special positions: 0 Unit cell: (138.55, 103.7, 68.85, 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 1251 8.00 N 1117 7.00 C 4024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS E 135 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 204 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " 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: 2.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1510 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 19 sheets defined 13.2% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'D' and resid 121 through 125 removed outlier: 3.618A pdb=" N LEU D 125 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.861A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.074A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.703A pdb=" N LEU E 197 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.545A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 53 " --> pdb=" O PRO A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 56 through 85 removed outlier: 3.620A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.173A pdb=" N THR A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 4.045A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 252 through 255 removed outlier: 4.498A pdb=" N GLN A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.937A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 67 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.512A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.735A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 114 through 115 removed outlier: 4.281A pdb=" N SER D 114 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 145 through 149 removed outlier: 4.351A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR D 197 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS D 149 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 193 " --> pdb=" O LYS D 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.076A pdb=" N SER D 174 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.871A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.530A pdb=" N VAL E 110 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 131 removed outlier: 3.521A pdb=" N SER E 128 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA E 145 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 192 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY E 147 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL E 190 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 149 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N SER E 188 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS E 151 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 186 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR E 153 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N SER E 187 " --> pdb=" O PRO E 175 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N VAL E 189 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 173 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 162 removed outlier: 4.269A pdb=" N CYS E 204 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS E 217 " --> pdb=" O CYS E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.861A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 124 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.573A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.573A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.536A pdb=" N VAL A 261 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.772A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.772A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 44 through 45 259 hydrogen bonds defined for protein. 660 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: 1.97 Time building geometry restraints manager: 2.31 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: 2110 1.34 - 1.46: 1654 1.46 - 1.58: 2778 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 6580 Sorted by residual: bond pdb=" CG ARG A 6 " pdb=" CD ARG A 6 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.506 1.453 0.053 3.90e-02 6.57e+02 1.82e+00 bond pdb=" SD MET E 108 " pdb=" CE MET E 108 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.79e+00 bond pdb=" CD LYS B 19 " pdb=" CE LYS B 19 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.73e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.56e+00 ... (remaining 6575 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.95: 130 105.95 - 112.97: 3501 112.97 - 119.99: 2189 119.99 - 127.02: 3009 127.02 - 134.04: 104 Bond angle restraints: 8933 Sorted by residual: angle pdb=" CA ARG E 218 " pdb=" CB ARG E 218 " pdb=" CG ARG E 218 " ideal model delta sigma weight residual 114.10 122.84 -8.74 2.00e+00 2.50e-01 1.91e+01 angle pdb=" N ARG A 17 " pdb=" CA ARG A 17 " pdb=" C ARG A 17 " ideal model delta sigma weight residual 107.49 116.40 -8.91 2.16e+00 2.14e-01 1.70e+01 angle pdb=" C GLU B 16 " pdb=" CA GLU B 16 " pdb=" CB GLU B 16 " ideal model delta sigma weight residual 109.70 117.03 -7.33 1.81e+00 3.05e-01 1.64e+01 angle pdb=" C LYS B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta sigma weight residual 121.81 129.99 -8.18 2.16e+00 2.14e-01 1.43e+01 angle pdb=" N ASN B 17 " pdb=" CA ASN B 17 " pdb=" C ASN B 17 " ideal model delta sigma weight residual 110.10 115.20 -5.10 1.49e+00 4.50e-01 1.17e+01 ... (remaining 8928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 3561 16.59 - 33.19: 283 33.19 - 49.78: 45 49.78 - 66.38: 11 66.38 - 82.97: 8 Dihedral angle restraints: 3908 sinusoidal: 1554 harmonic: 2354 Sorted by residual: dihedral pdb=" CB CYS E 148 " pdb=" SG CYS E 148 " pdb=" SG CYS E 204 " pdb=" CB CYS E 204 " ideal model delta sinusoidal sigma weight residual 93.00 143.03 -50.03 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 52.16 40.84 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS B 25 " pdb=" SG CYS B 25 " pdb=" SG CYS B 80 " pdb=" CB CYS B 80 " ideal model delta sinusoidal sigma weight residual -86.00 -113.49 27.49 1 1.00e+01 1.00e-02 1.08e+01 ... (remaining 3905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 587 0.040 - 0.080: 266 0.080 - 0.119: 68 0.119 - 0.159: 29 0.159 - 0.199: 7 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA LYS B 19 " pdb=" N LYS B 19 " pdb=" C LYS B 19 " pdb=" CB LYS B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR E 173 " pdb=" CA THR E 173 " pdb=" OG1 THR E 173 " pdb=" CG2 THR E 173 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB ILE D 106 " pdb=" CA ILE D 106 " pdb=" CG1 ILE D 106 " pdb=" CG2 ILE D 106 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 954 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 174 " -0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO E 175 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 175 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 175 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO D 80 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 19 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 20 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 20 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 20 " 0.037 5.00e-02 4.00e+02 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 914 2.76 - 3.29: 5434 3.29 - 3.83: 9750 3.83 - 4.36: 12022 4.36 - 4.90: 21803 Nonbonded interactions: 49923 Sorted by model distance: nonbonded pdb=" O GLN A 255 " pdb=" NH2 ARG A 273 " model vdw 2.220 2.520 nonbonded pdb=" NE2 GLN D 147 " pdb=" O GLN D 155 " model vdw 2.288 2.520 nonbonded pdb=" OD2 ASP A 220 " pdb=" NH1 ARG A 256 " model vdw 2.295 2.520 nonbonded pdb=" O SER E 196 " pdb=" OG SER E 196 " model vdw 2.321 2.440 nonbonded pdb=" O GLN D 124 " pdb=" OG SER D 127 " model vdw 2.331 2.440 ... (remaining 49918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.120 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: 13.040 Check model and map are aligned: 0.000 Set scattering table: 0.770 Process input model: 21.070 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: 0.010 Load rotamer database and sin/cos tables:18.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.007 0.053 6580 Z= 0.453 Angle : 0.818 8.907 8933 Z= 0.432 Chirality : 0.051 0.199 957 Planarity : 0.006 0.096 1157 Dihedral : 12.620 82.970 2374 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.27), residues: 800 helix: -1.37 (0.52), residues: 79 sheet: -1.37 (0.27), residues: 333 loop : -2.06 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 100 HIS 0.007 0.001 HIS E 208 PHE 0.031 0.002 PHE B 70 TYR 0.025 0.002 TYR A 113 ARG 0.014 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: E 73 ASP cc_start: 0.8497 (t70) cc_final: 0.8252 (t70) REVERT: E 108 MET cc_start: 0.8701 (mpp) cc_final: 0.8219 (mpt) REVERT: A 173 GLU cc_start: 0.8080 (tp30) cc_final: 0.7730 (tp30) REVERT: A 219 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8290 (ttt-90) REVERT: A 255 GLN cc_start: 0.9172 (mm110) cc_final: 0.8836 (mm110) REVERT: B 76 ASP cc_start: 0.8614 (m-30) cc_final: 0.8387 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.7165 time to fit residues: 147.7013 Evaluate side-chains 76 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN B 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6580 Z= 0.232 Angle : 0.592 6.614 8933 Z= 0.314 Chirality : 0.044 0.147 957 Planarity : 0.005 0.068 1157 Dihedral : 4.688 21.780 890 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.14 % Allowed : 7.54 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.29), residues: 800 helix: -0.38 (0.57), residues: 78 sheet: -0.66 (0.28), residues: 339 loop : -1.47 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 100 HIS 0.003 0.001 HIS E 208 PHE 0.013 0.001 PHE B 70 TYR 0.013 0.001 TYR A 99 ARG 0.006 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.723 Fit side-chains REVERT: A 58 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 121 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8596 (ptpp) REVERT: A 173 GLU cc_start: 0.8130 (tp30) cc_final: 0.7797 (tp30) REVERT: A 255 GLN cc_start: 0.9189 (mm110) cc_final: 0.8842 (mm110) outliers start: 8 outliers final: 1 residues processed: 71 average time/residue: 1.8289 time to fit residues: 134.6000 Evaluate side-chains 67 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 6580 Z= 0.372 Angle : 0.604 5.727 8933 Z= 0.320 Chirality : 0.045 0.171 957 Planarity : 0.005 0.067 1157 Dihedral : 4.799 26.382 890 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.28 % Allowed : 10.38 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.29), residues: 800 helix: -0.29 (0.58), residues: 78 sheet: -0.27 (0.28), residues: 347 loop : -1.29 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 100 HIS 0.005 0.001 HIS E 95 PHE 0.019 0.002 PHE B 70 TYR 0.015 0.002 TYR B 63 ARG 0.005 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: A 113 TYR cc_start: 0.7794 (m-80) cc_final: 0.7585 (m-80) REVERT: A 121 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8630 (ptpp) REVERT: A 173 GLU cc_start: 0.8155 (tp30) cc_final: 0.7779 (tp30) REVERT: A 219 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8364 (ttt-90) REVERT: A 255 GLN cc_start: 0.9182 (mm110) cc_final: 0.8863 (mm110) REVERT: B 19 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8870 (ptpp) REVERT: B 44 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: B 76 ASP cc_start: 0.8652 (m-30) cc_final: 0.8358 (m-30) outliers start: 9 outliers final: 2 residues processed: 69 average time/residue: 1.7145 time to fit residues: 123.2200 Evaluate side-chains 69 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain B residue 44 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 40.0000 chunk 64 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8563 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6580 Z= 0.313 Angle : 0.560 5.210 8933 Z= 0.297 Chirality : 0.044 0.160 957 Planarity : 0.005 0.063 1157 Dihedral : 4.660 26.296 890 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.56 % Allowed : 12.38 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 800 helix: 0.42 (0.61), residues: 72 sheet: 0.10 (0.29), residues: 328 loop : -1.18 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 100 HIS 0.004 0.001 HIS E 95 PHE 0.013 0.002 PHE B 70 TYR 0.013 0.001 TYR B 63 ARG 0.004 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: E 89 GLU cc_start: 0.8921 (pm20) cc_final: 0.8335 (pm20) REVERT: A 58 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: A 113 TYR cc_start: 0.7823 (m-80) cc_final: 0.7608 (m-80) REVERT: A 121 LYS cc_start: 0.8969 (ptpp) cc_final: 0.8705 (ptpp) REVERT: A 219 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8371 (ttt-90) REVERT: A 255 GLN cc_start: 0.9188 (mm110) cc_final: 0.8890 (mm110) REVERT: B 76 ASP cc_start: 0.8664 (m-30) cc_final: 0.8330 (m-30) REVERT: B 96 ASP cc_start: 0.8252 (t0) cc_final: 0.8045 (t0) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 1.6556 time to fit residues: 118.9652 Evaluate side-chains 68 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6580 Z= 0.287 Angle : 0.542 5.088 8933 Z= 0.288 Chirality : 0.043 0.156 957 Planarity : 0.004 0.060 1157 Dihedral : 4.575 27.452 890 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.13 % Allowed : 12.52 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.29), residues: 800 helix: 0.58 (0.61), residues: 72 sheet: 0.23 (0.29), residues: 328 loop : -1.08 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 100 HIS 0.004 0.001 HIS E 95 PHE 0.013 0.002 PHE D 91 TYR 0.012 0.001 TYR B 63 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: E 125 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7448 (tmtp) REVERT: E 183 LEU cc_start: 0.8562 (mm) cc_final: 0.8288 (mm) REVERT: A 58 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: A 113 TYR cc_start: 0.7835 (m-80) cc_final: 0.7592 (m-80) REVERT: A 121 LYS cc_start: 0.8959 (ptpp) cc_final: 0.8688 (ptpp) REVERT: A 219 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8358 (ttt-90) REVERT: A 255 GLN cc_start: 0.9166 (mm110) cc_final: 0.8902 (mm110) REVERT: B 76 ASP cc_start: 0.8702 (m-30) cc_final: 0.8469 (m-30) REVERT: B 94 LYS cc_start: 0.9011 (mttt) cc_final: 0.8774 (mttm) REVERT: B 96 ASP cc_start: 0.8283 (t0) cc_final: 0.8053 (t0) outliers start: 15 outliers final: 8 residues processed: 71 average time/residue: 1.7027 time to fit residues: 126.0286 Evaluate side-chains 70 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 30.0000 chunk 77 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8537 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6580 Z= 0.209 Angle : 0.505 5.151 8933 Z= 0.269 Chirality : 0.042 0.142 957 Planarity : 0.004 0.056 1157 Dihedral : 4.352 25.565 890 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.56 % Allowed : 13.51 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.30), residues: 800 helix: 0.91 (0.62), residues: 72 sheet: 0.35 (0.29), residues: 328 loop : -0.94 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE D 91 TYR 0.011 0.001 TYR A 99 ARG 0.003 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.755 Fit side-chains REVERT: E 183 LEU cc_start: 0.8571 (mm) cc_final: 0.8315 (mm) REVERT: A 58 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 113 TYR cc_start: 0.7799 (m-80) cc_final: 0.7587 (m-80) REVERT: A 121 LYS cc_start: 0.8867 (ptpp) cc_final: 0.8606 (ptpp) REVERT: A 219 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8347 (ttt-90) REVERT: A 255 GLN cc_start: 0.9128 (mm110) cc_final: 0.8829 (mm110) REVERT: B 94 LYS cc_start: 0.9017 (mttt) cc_final: 0.8683 (mttm) REVERT: B 96 ASP cc_start: 0.8261 (t0) cc_final: 0.7806 (t0) REVERT: B 99 MET cc_start: 0.7641 (ttm) cc_final: 0.7336 (ttp) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 1.6112 time to fit residues: 117.6091 Evaluate side-chains 65 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6580 Z= 0.214 Angle : 0.509 4.980 8933 Z= 0.271 Chirality : 0.042 0.144 957 Planarity : 0.004 0.054 1157 Dihedral : 4.287 24.566 890 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.99 % Allowed : 13.66 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.30), residues: 800 helix: 0.97 (0.62), residues: 72 sheet: 0.42 (0.29), residues: 328 loop : -0.87 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE D 91 TYR 0.011 0.001 TYR A 99 ARG 0.004 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.818 Fit side-chains REVERT: E 125 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7456 (tmtp) REVERT: E 183 LEU cc_start: 0.8497 (mm) cc_final: 0.8219 (mm) REVERT: A 58 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 121 LYS cc_start: 0.8860 (ptpp) cc_final: 0.8596 (ptpp) REVERT: A 219 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8338 (ttt-90) REVERT: A 255 GLN cc_start: 0.9132 (mm110) cc_final: 0.8827 (mm110) REVERT: B 94 LYS cc_start: 0.9019 (mttt) cc_final: 0.8690 (mttm) REVERT: B 96 ASP cc_start: 0.8297 (t0) cc_final: 0.7934 (t0) REVERT: B 99 MET cc_start: 0.7686 (ttm) cc_final: 0.7364 (ttp) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 1.7454 time to fit residues: 121.8781 Evaluate side-chains 67 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.0010 chunk 15 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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: 0.8517 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6580 Z= 0.165 Angle : 0.482 4.925 8933 Z= 0.257 Chirality : 0.041 0.138 957 Planarity : 0.004 0.053 1157 Dihedral : 4.117 22.269 890 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.56 % Allowed : 14.65 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 800 helix: 1.22 (0.62), residues: 72 sheet: 0.49 (0.29), residues: 328 loop : -0.75 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 100 HIS 0.003 0.001 HIS E 35 PHE 0.009 0.001 PHE D 91 TYR 0.011 0.001 TYR A 99 ARG 0.005 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.736 Fit side-chains REVERT: E 125 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7456 (tmtp) REVERT: E 183 LEU cc_start: 0.8529 (mm) cc_final: 0.8295 (mm) REVERT: A 58 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 121 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8588 (ptpp) REVERT: A 255 GLN cc_start: 0.9116 (mm110) cc_final: 0.8839 (mm-40) REVERT: B 19 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8697 (ptpp) REVERT: B 94 LYS cc_start: 0.9018 (mttt) cc_final: 0.8704 (mttm) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 1.6021 time to fit residues: 106.9602 Evaluate side-chains 66 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6580 Z= 0.140 Angle : 0.470 5.056 8933 Z= 0.250 Chirality : 0.041 0.137 957 Planarity : 0.004 0.053 1157 Dihedral : 3.927 16.633 890 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 15.36 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 800 helix: 1.44 (0.63), residues: 72 sheet: 0.43 (0.30), residues: 325 loop : -0.59 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.000 HIS E 35 PHE 0.008 0.001 PHE A 33 TYR 0.010 0.001 TYR A 99 ARG 0.006 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.744 Fit side-chains REVERT: E 125 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7396 (tmtp) REVERT: E 183 LEU cc_start: 0.8541 (mm) cc_final: 0.8315 (mm) REVERT: A 58 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 121 LYS cc_start: 0.8805 (ptpp) cc_final: 0.8567 (ptpp) REVERT: B 19 LYS cc_start: 0.8898 (ptpp) cc_final: 0.8674 (ptpp) REVERT: B 94 LYS cc_start: 0.9017 (mttt) cc_final: 0.8710 (mttm) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 1.7643 time to fit residues: 128.3666 Evaluate side-chains 71 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6580 Z= 0.315 Angle : 0.549 5.260 8933 Z= 0.290 Chirality : 0.043 0.163 957 Planarity : 0.005 0.052 1157 Dihedral : 4.265 17.060 890 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.28 % Allowed : 15.65 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.30), residues: 800 helix: 0.98 (0.61), residues: 72 sheet: 0.40 (0.29), residues: 327 loop : -0.63 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 100 HIS 0.004 0.001 HIS E 95 PHE 0.014 0.002 PHE D 91 TYR 0.015 0.001 TYR B 63 ARG 0.011 0.001 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: E 125 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7377 (tmtp) REVERT: E 183 LEU cc_start: 0.8514 (mm) cc_final: 0.8274 (mm) REVERT: A 58 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: A 121 LYS cc_start: 0.8939 (ptpp) cc_final: 0.8644 (ptpp) REVERT: B 19 LYS cc_start: 0.9038 (ptpp) cc_final: 0.8785 (ptpp) REVERT: B 94 LYS cc_start: 0.9036 (mttt) cc_final: 0.8616 (mttm) REVERT: B 96 ASP cc_start: 0.8292 (t0) cc_final: 0.8040 (t0) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 1.7371 time to fit residues: 119.4385 Evaluate side-chains 65 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 0.0070 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.141324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.078457 restraints weight = 8510.519| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.70 r_work: 0.2721 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6580 Z= 0.157 Angle : 0.488 5.033 8933 Z= 0.259 Chirality : 0.041 0.134 957 Planarity : 0.004 0.053 1157 Dihedral : 4.059 16.627 890 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.14 % Allowed : 16.07 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 800 helix: 1.38 (0.63), residues: 72 sheet: 0.47 (0.29), residues: 325 loop : -0.49 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 244 HIS 0.003 0.001 HIS E 35 PHE 0.008 0.001 PHE D 91 TYR 0.011 0.001 TYR A 99 ARG 0.013 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.25 seconds wall clock time: 54 minutes 1.54 seconds (3241.54 seconds total)