Starting phenix.real_space_refine on Fri Feb 14 21:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rpw_24624/02_2025/7rpw_24624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpw_24624/02_2025/7rpw_24624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/02_2025/7rpw_24624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpw_24624/02_2025/7rpw_24624.map" model { file = "/net/cci-nas-00/data/ceres_data/7rpw_24624/02_2025/7rpw_24624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpw_24624/02_2025/7rpw_24624.cif" } resolution = 4.38 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= 0.001 sd= 0.101 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 S 25 5.16 5 C 6567 2.51 5 N 1750 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10594 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1941 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "X" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "Z" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3480 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 425} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.90, per 1000 atoms: 0.56 Number of scatterers: 10594 At special positions: 0 Unit cell: (117, 106.5, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 25 16.00 P 63 15.00 O 2185 8.00 N 1750 7.00 C 6567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.3 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 28.1% alpha, 16.5% beta 30 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.712A pdb=" N ILE A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.864A pdb=" N ASN A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.501A pdb=" N VAL B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 removed outlier: 4.131A pdb=" N LEU B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.584A pdb=" N VAL B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.705A pdb=" N ASP C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 18 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.662A pdb=" N ILE C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 79 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 4.070A pdb=" N LYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 removed outlier: 4.706A pdb=" N ILE E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 33 removed outlier: 3.804A pdb=" N THR E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 47 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.522A pdb=" N LEU E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.840A pdb=" N ARG E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 133 removed outlier: 4.304A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 removed outlier: 4.557A pdb=" N LEU E 142 " --> pdb=" O GLY E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 4.067A pdb=" N ARG E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 removed outlier: 3.514A pdb=" N VAL E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 204 removed outlier: 4.544A pdb=" N ILE E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 217 Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 291 through 300 removed outlier: 4.118A pdb=" N TYR E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 331 removed outlier: 4.102A pdb=" N HIS E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG E 330 " --> pdb=" O GLU E 326 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 375 removed outlier: 3.636A pdb=" N GLU E 373 " --> pdb=" O ARG E 369 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.646A pdb=" N ILE A 89 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 92 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 99 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 175 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 112 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 173 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 4.116A pdb=" N ILE A 35 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 38 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 27 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 40 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N SER A 25 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 70 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 28 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138 removed outlier: 3.622A pdb=" N VAL A 134 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.603A pdb=" N ALA A 179 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.670A pdb=" N THR B 99 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.630A pdb=" N ASP B 49 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 51 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR B 236 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.694A pdb=" N SER B 189 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 132 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AB1, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.620A pdb=" N PHE B 165 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 97 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 87 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 5 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 4.749A pdb=" N VAL C 26 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 37 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 51 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 47 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 46 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.516A pdb=" N PHE C 218 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.890A pdb=" N SER C 192 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 241 removed outlier: 6.364A pdb=" N GLU E 239 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 275 through 278 removed outlier: 4.203A pdb=" N ILE E 307 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE E 306 " --> pdb=" O MET E 353 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2810 1.33 - 1.45: 1960 1.45 - 1.57: 5949 1.57 - 1.69: 122 1.69 - 1.81: 50 Bond restraints: 10891 Sorted by residual: bond pdb=" C3' DA Z 22 " pdb=" O3' DA Z 22 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.02e+00 bond pdb=" C4' AMP Y 101 " pdb=" O4' AMP Y 101 " ideal model delta sigma weight residual 1.454 1.431 0.023 1.50e-02 4.44e+03 2.37e+00 bond pdb=" C3' DA Z 13 " pdb=" O3' DA Z 13 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" C1' AMP Y 101 " pdb=" N9 AMP Y 101 " ideal model delta sigma weight residual 1.465 1.483 -0.018 1.50e-02 4.44e+03 1.48e+00 bond pdb=" C2' AMP Y 101 " pdb=" O2' AMP Y 101 " ideal model delta sigma weight residual 1.412 1.429 -0.017 1.50e-02 4.44e+03 1.32e+00 ... (remaining 10886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14372 1.25 - 2.50: 463 2.50 - 3.75: 92 3.75 - 5.00: 21 5.00 - 6.25: 6 Bond angle restraints: 14954 Sorted by residual: angle pdb=" C1' AMP Y 101 " pdb=" C2' AMP Y 101 " pdb=" C3' AMP Y 101 " ideal model delta sigma weight residual 101.50 105.38 -3.88 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N GLU E 366 " pdb=" CA GLU E 366 " pdb=" C GLU E 366 " ideal model delta sigma weight residual 113.18 109.01 4.17 1.33e+00 5.65e-01 9.81e+00 angle pdb=" C3' AMP Y 101 " pdb=" C2' AMP Y 101 " pdb=" O2' AMP Y 101 " ideal model delta sigma weight residual 114.60 110.03 4.57 1.50e+00 4.44e-01 9.29e+00 angle pdb=" C2' AMP Y 101 " pdb=" C3' AMP Y 101 " pdb=" C4' AMP Y 101 " ideal model delta sigma weight residual 102.60 105.50 -2.90 1.00e+00 1.00e+00 8.43e+00 angle pdb=" C2' AMP Y 101 " pdb=" C1' AMP Y 101 " pdb=" N9 AMP Y 101 " ideal model delta sigma weight residual 114.00 109.91 4.09 1.50e+00 4.44e-01 7.44e+00 ... (remaining 14949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 6066 34.68 - 69.36: 385 69.36 - 104.04: 5 104.04 - 138.72: 0 138.72 - 173.39: 5 Dihedral angle restraints: 6461 sinusoidal: 3029 harmonic: 3432 Sorted by residual: dihedral pdb=" CA SER E 139 " pdb=" C SER E 139 " pdb=" N ARG E 140 " pdb=" CA ARG E 140 " ideal model delta harmonic sigma weight residual 180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LEU C 205 " pdb=" C LEU C 205 " pdb=" N SER C 206 " pdb=" CA SER C 206 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU C 11 " pdb=" C LEU C 11 " pdb=" N LYS C 12 " pdb=" CA LYS C 12 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1173 0.035 - 0.069: 372 0.069 - 0.104: 120 0.104 - 0.139: 57 0.139 - 0.173: 2 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CB VAL C 244 " pdb=" CA VAL C 244 " pdb=" CG1 VAL C 244 " pdb=" CG2 VAL C 244 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" P DG Z 27 " pdb=" OP1 DG Z 27 " pdb=" OP2 DG Z 27 " pdb=" O5' DG Z 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE E 231 " pdb=" N ILE E 231 " pdb=" C ILE E 231 " pdb=" CB ILE E 231 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1721 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 93 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.39e+00 pdb=" N PRO C 94 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 94 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 94 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 226 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO E 227 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 121 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO B 122 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.016 5.00e-02 4.00e+02 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 62 2.38 - 3.01: 6110 3.01 - 3.64: 17020 3.64 - 4.27: 23587 4.27 - 4.90: 36833 Nonbonded interactions: 83612 Sorted by model distance: nonbonded pdb=" O GLY E 60 " pdb="MN MN X 101 " model vdw 1.756 2.320 nonbonded pdb=" OP1 DG X 22 " pdb="MN MN E 701 " model vdw 1.835 2.320 nonbonded pdb=" O3' DG X 20 " pdb="MN MN X 101 " model vdw 1.913 2.320 nonbonded pdb=" O LYS E 130 " pdb=" OG1 THR E 134 " model vdw 2.077 3.040 nonbonded pdb=" OP1 DC X 21 " pdb="MN MN X 102 " model vdw 2.146 2.320 ... (remaining 83607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.003 0.052 10891 Z= 0.205 Angle : 0.570 6.255 14954 Z= 0.315 Chirality : 0.042 0.173 1724 Planarity : 0.003 0.029 1681 Dihedral : 19.295 173.395 4243 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.27 % Favored : 88.64 % Rotamer: Outliers : 9.97 % Allowed : 13.46 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.24), residues: 1171 helix: -0.42 (0.30), residues: 300 sheet: -1.68 (0.31), residues: 304 loop : -2.82 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 50 HIS 0.005 0.001 HIS B 157 PHE 0.018 0.001 PHE E 53 TYR 0.010 0.001 TYR C 196 ARG 0.004 0.000 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 153 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.8094 (t) cc_final: 0.7567 (m) REVERT: A 80 SER cc_start: 0.9022 (t) cc_final: 0.8779 (p) REVERT: A 137 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 21 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7684 (t0) REVERT: B 89 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4884 (tp) REVERT: C 44 ILE cc_start: 0.9077 (mt) cc_final: 0.8816 (mm) REVERT: C 75 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: C 146 VAL cc_start: 0.7875 (t) cc_final: 0.6797 (t) REVERT: E 123 GLU cc_start: 0.7720 (pp20) cc_final: 0.7429 (mp0) REVERT: E 142 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (mp) REVERT: E 164 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7698 (tpt170) REVERT: E 328 MET cc_start: 0.8601 (mtm) cc_final: 0.7994 (tmm) REVERT: E 360 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.4463 (t80) REVERT: E 372 LEU cc_start: 0.6464 (tp) cc_final: 0.6179 (tp) outliers start: 103 outliers final: 40 residues processed: 239 average time/residue: 0.2337 time to fit residues: 78.4641 Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 0.0170 chunk 110 optimal weight: 5.9990 overall best weight: 1.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN E 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.115753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.098053 restraints weight = 46513.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.098848 restraints weight = 36989.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.099475 restraints weight = 32249.397| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3944 r_free = 0.3944 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3943 r_free = 0.3943 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10891 Z= 0.211 Angle : 0.642 6.264 14954 Z= 0.348 Chirality : 0.046 0.271 1724 Planarity : 0.004 0.035 1681 Dihedral : 22.083 175.539 1931 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.25 % Favored : 89.67 % Rotamer: Outliers : 0.19 % Allowed : 3.97 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.24), residues: 1171 helix: -0.50 (0.29), residues: 308 sheet: -1.48 (0.31), residues: 309 loop : -2.77 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 50 HIS 0.004 0.001 HIS B 157 PHE 0.023 0.002 PHE E 53 TYR 0.015 0.002 TYR B 56 ARG 0.005 0.001 ARG E 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7370 (mp) cc_final: 0.6599 (mp) REVERT: A 80 SER cc_start: 0.8980 (t) cc_final: 0.8751 (p) REVERT: B 136 LEU cc_start: 0.7383 (tp) cc_final: 0.6975 (tp) REVERT: B 146 GLU cc_start: 0.6501 (mt-10) cc_final: 0.6197 (tt0) REVERT: B 216 GLU cc_start: 0.3779 (mm-30) cc_final: 0.3492 (mm-30) REVERT: C 1 MET cc_start: 0.7738 (tpt) cc_final: 0.7179 (tpp) REVERT: C 44 ILE cc_start: 0.8794 (mt) cc_final: 0.8546 (mm) REVERT: C 80 VAL cc_start: 0.7506 (m) cc_final: 0.6019 (m) REVERT: E 8 GLU cc_start: 0.7807 (tm-30) cc_final: 0.6802 (pt0) REVERT: E 63 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7467 (mt-10) REVERT: E 133 LEU cc_start: 0.7595 (mp) cc_final: 0.7259 (mt) REVERT: E 164 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7709 (mmt-90) REVERT: E 360 TYR cc_start: 0.6061 (m-10) cc_final: 0.5770 (t80) REVERT: E 372 LEU cc_start: 0.6387 (tp) cc_final: 0.6116 (tp) outliers start: 2 outliers final: 0 residues processed: 158 average time/residue: 0.2504 time to fit residues: 55.1080 Evaluate side-chains 98 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 120 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 117 optimal weight: 0.0060 chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.116398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.098258 restraints weight = 46586.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.099446 restraints weight = 40588.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.099846 restraints weight = 34669.603| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10891 Z= 0.192 Angle : 0.607 6.285 14954 Z= 0.327 Chirality : 0.044 0.180 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.122 174.428 1931 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.39 % Favored : 90.52 % Rotamer: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.24), residues: 1171 helix: -0.27 (0.30), residues: 297 sheet: -1.56 (0.31), residues: 309 loop : -2.71 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 50 HIS 0.002 0.001 HIS B 157 PHE 0.017 0.002 PHE E 53 TYR 0.027 0.001 TYR A 200 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7341 (t80) cc_final: 0.7096 (t80) REVERT: A 40 LEU cc_start: 0.7165 (mp) cc_final: 0.6963 (mp) REVERT: A 80 SER cc_start: 0.9049 (t) cc_final: 0.8796 (p) REVERT: A 163 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8594 (mp0) REVERT: B 129 PHE cc_start: 0.6717 (m-10) cc_final: 0.6433 (m-80) REVERT: B 146 GLU cc_start: 0.6552 (mt-10) cc_final: 0.5938 (tt0) REVERT: B 216 GLU cc_start: 0.4213 (mm-30) cc_final: 0.4007 (mm-30) REVERT: C 44 ILE cc_start: 0.8847 (mt) cc_final: 0.8568 (mm) REVERT: C 80 VAL cc_start: 0.7484 (m) cc_final: 0.6107 (m) REVERT: C 150 THR cc_start: 0.8702 (p) cc_final: 0.8407 (t) REVERT: E 8 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6825 (pt0) REVERT: E 63 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7497 (mt-10) REVERT: E 133 LEU cc_start: 0.7633 (mp) cc_final: 0.7321 (mt) REVERT: E 372 LEU cc_start: 0.6382 (tp) cc_final: 0.6155 (tp) REVERT: E 381 TYR cc_start: 0.7388 (m-80) cc_final: 0.7157 (m-80) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.2452 time to fit residues: 44.1781 Evaluate side-chains 94 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.114604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.096311 restraints weight = 46236.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.097598 restraints weight = 41044.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.098095 restraints weight = 34280.480| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10891 Z= 0.216 Angle : 0.618 6.662 14954 Z= 0.331 Chirality : 0.045 0.152 1724 Planarity : 0.003 0.030 1681 Dihedral : 22.138 173.752 1931 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.93 % Favored : 88.98 % Rotamer: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.24), residues: 1171 helix: -0.31 (0.30), residues: 302 sheet: -1.55 (0.32), residues: 293 loop : -2.82 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 50 HIS 0.004 0.001 HIS B 157 PHE 0.020 0.002 PHE C 139 TYR 0.027 0.002 TYR C 59 ARG 0.005 0.001 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9089 (t) cc_final: 0.8791 (p) REVERT: A 229 MET cc_start: 0.7645 (mmm) cc_final: 0.7045 (mmm) REVERT: B 36 ARG cc_start: 0.7452 (mmt180) cc_final: 0.7023 (mmt90) REVERT: B 129 PHE cc_start: 0.6854 (m-10) cc_final: 0.6584 (m-80) REVERT: B 136 LEU cc_start: 0.7660 (tp) cc_final: 0.7440 (tp) REVERT: C 1 MET cc_start: 0.7625 (tpp) cc_final: 0.7420 (tpp) REVERT: C 44 ILE cc_start: 0.8877 (mt) cc_final: 0.8588 (mm) REVERT: C 75 MET cc_start: 0.8197 (mmt) cc_final: 0.7808 (tpp) REVERT: C 140 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7940 (tmtt) REVERT: C 150 THR cc_start: 0.8676 (p) cc_final: 0.8407 (t) REVERT: E 8 GLU cc_start: 0.7925 (tm-30) cc_final: 0.6938 (pt0) REVERT: E 63 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7503 (mt-10) REVERT: E 123 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7375 (mm-30) REVERT: E 372 LEU cc_start: 0.6221 (tp) cc_final: 0.5891 (tp) REVERT: E 381 TYR cc_start: 0.7436 (m-80) cc_final: 0.7169 (m-80) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.2390 time to fit residues: 41.5268 Evaluate side-chains 92 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.107829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.089068 restraints weight = 46089.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.090197 restraints weight = 36241.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.090500 restraints weight = 32100.839| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3814 r_free = 0.3814 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10891 Z= 0.330 Angle : 0.728 9.251 14954 Z= 0.387 Chirality : 0.048 0.183 1724 Planarity : 0.004 0.035 1681 Dihedral : 22.269 172.290 1931 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.07 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.23), residues: 1171 helix: -0.61 (0.29), residues: 294 sheet: -1.84 (0.30), residues: 316 loop : -3.02 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP E 50 HIS 0.008 0.002 HIS B 157 PHE 0.027 0.002 PHE E 165 TYR 0.033 0.002 TYR C 59 ARG 0.005 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9097 (t) cc_final: 0.8791 (p) REVERT: A 229 MET cc_start: 0.7876 (mmm) cc_final: 0.7167 (mmm) REVERT: B 36 ARG cc_start: 0.7324 (mmt180) cc_final: 0.6836 (mmt90) REVERT: B 136 LEU cc_start: 0.7440 (tp) cc_final: 0.7131 (tp) REVERT: B 216 GLU cc_start: 0.4754 (mm-30) cc_final: 0.4393 (mm-30) REVERT: C 1 MET cc_start: 0.7536 (tpp) cc_final: 0.7128 (tpp) REVERT: C 44 ILE cc_start: 0.8706 (mt) cc_final: 0.8442 (mm) REVERT: C 140 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8082 (tmtt) REVERT: C 213 TYR cc_start: 0.8085 (m-80) cc_final: 0.7526 (m-80) REVERT: C 230 MET cc_start: 0.4597 (mmt) cc_final: 0.3801 (mmt) REVERT: E 8 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7201 (pt0) REVERT: E 25 LEU cc_start: 0.9185 (mm) cc_final: 0.8935 (pp) REVERT: E 63 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7464 (mt-10) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2206 time to fit residues: 34.6728 Evaluate side-chains 82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 14 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 60 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 HIS E 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.113630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.095831 restraints weight = 46499.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.095962 restraints weight = 38043.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.096607 restraints weight = 35882.813| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10891 Z= 0.197 Angle : 0.616 6.362 14954 Z= 0.331 Chirality : 0.044 0.176 1724 Planarity : 0.003 0.035 1681 Dihedral : 22.209 173.545 1931 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.42 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -2.84 (0.24), residues: 1171 helix: -0.48 (0.30), residues: 297 sheet: -1.53 (0.31), residues: 304 loop : -2.92 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 50 HIS 0.005 0.001 HIS B 157 PHE 0.021 0.002 PHE C 228 TYR 0.025 0.001 TYR C 59 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9095 (t) cc_final: 0.8762 (m) REVERT: A 229 MET cc_start: 0.8106 (mmm) cc_final: 0.7374 (mmm) REVERT: B 36 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6812 (mmt90) REVERT: B 216 GLU cc_start: 0.4735 (mm-30) cc_final: 0.4390 (mm-30) REVERT: C 1 MET cc_start: 0.7308 (tpp) cc_final: 0.6996 (tpp) REVERT: C 44 ILE cc_start: 0.8683 (mt) cc_final: 0.8425 (mm) REVERT: C 150 THR cc_start: 0.8586 (p) cc_final: 0.8381 (t) REVERT: C 213 TYR cc_start: 0.8047 (m-80) cc_final: 0.7456 (m-80) REVERT: E 8 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7014 (pt0) REVERT: E 25 LEU cc_start: 0.9099 (mm) cc_final: 0.8886 (pp) REVERT: E 63 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7343 (mt-10) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2336 time to fit residues: 40.1537 Evaluate side-chains 85 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 120 optimal weight: 40.0000 chunk 75 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.113104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.093383 restraints weight = 50626.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.093828 restraints weight = 39746.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.094398 restraints weight = 33636.033| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10891 Z= 0.317 Angle : 0.713 9.588 14954 Z= 0.378 Chirality : 0.047 0.161 1724 Planarity : 0.004 0.038 1681 Dihedral : 22.260 172.475 1931 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.24 % Favored : 86.68 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.23), residues: 1171 helix: -0.87 (0.28), residues: 303 sheet: -1.79 (0.30), residues: 311 loop : -3.05 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 50 HIS 0.009 0.001 HIS B 157 PHE 0.022 0.002 PHE C 228 TYR 0.033 0.002 TYR C 59 ARG 0.004 0.001 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9091 (t) cc_final: 0.8768 (p) REVERT: B 136 LEU cc_start: 0.7202 (tp) cc_final: 0.6936 (tp) REVERT: B 216 GLU cc_start: 0.4882 (mm-30) cc_final: 0.4640 (mm-30) REVERT: C 1 MET cc_start: 0.7145 (tpp) cc_final: 0.6882 (tpp) REVERT: C 44 ILE cc_start: 0.8669 (mt) cc_final: 0.8440 (mm) REVERT: E 8 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7153 (pt0) REVERT: E 63 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7382 (mt-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2186 time to fit residues: 33.1371 Evaluate side-chains 79 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 267 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 = 0.4216 r_free = 0.4216 target = 0.112740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.094712 restraints weight = 46682.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.095204 restraints weight = 37936.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.095631 restraints weight = 37339.066| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10891 Z= 0.220 Angle : 0.639 8.854 14954 Z= 0.340 Chirality : 0.045 0.166 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.230 173.283 1931 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.42 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.23), residues: 1171 helix: -0.58 (0.30), residues: 295 sheet: -1.52 (0.31), residues: 296 loop : -3.03 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 50 HIS 0.004 0.001 HIS B 157 PHE 0.023 0.002 PHE C 228 TYR 0.026 0.002 TYR C 59 ARG 0.005 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9132 (t) cc_final: 0.8793 (m) REVERT: A 229 MET cc_start: 0.7238 (mmp) cc_final: 0.7015 (tpp) REVERT: B 36 ARG cc_start: 0.7367 (mmt180) cc_final: 0.6980 (mmt180) REVERT: B 121 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 126 ASN cc_start: 0.7417 (t0) cc_final: 0.7146 (t0) REVERT: B 216 GLU cc_start: 0.4216 (mm-30) cc_final: 0.3976 (mm-30) REVERT: C 1 MET cc_start: 0.7219 (tpp) cc_final: 0.6860 (tpp) REVERT: C 44 ILE cc_start: 0.8700 (mt) cc_final: 0.8415 (mm) REVERT: C 75 MET cc_start: 0.7989 (tpp) cc_final: 0.7619 (tpp) REVERT: E 8 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7236 (pt0) REVERT: E 63 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7340 (mt-10) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2389 time to fit residues: 36.4971 Evaluate side-chains 84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.113933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.096076 restraints weight = 47693.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.097001 restraints weight = 41929.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.097568 restraints weight = 35163.895| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3912 r_free = 0.3912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10891 Z= 0.194 Angle : 0.609 8.730 14954 Z= 0.326 Chirality : 0.044 0.166 1724 Planarity : 0.003 0.035 1681 Dihedral : 22.176 173.799 1931 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.85 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.24), residues: 1171 helix: -0.48 (0.30), residues: 296 sheet: -1.39 (0.32), residues: 291 loop : -3.00 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP E 50 HIS 0.004 0.001 HIS B 157 PHE 0.027 0.002 PHE C 139 TYR 0.028 0.001 TYR C 59 ARG 0.006 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9117 (t) cc_final: 0.8769 (m) REVERT: A 229 MET cc_start: 0.7495 (mmp) cc_final: 0.7287 (tpp) REVERT: B 36 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6923 (mmt180) REVERT: B 121 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 126 ASN cc_start: 0.7294 (t0) cc_final: 0.6966 (t0) REVERT: B 216 GLU cc_start: 0.4147 (mm-30) cc_final: 0.3890 (mm-30) REVERT: C 1 MET cc_start: 0.7150 (tpp) cc_final: 0.6861 (tpp) REVERT: C 44 ILE cc_start: 0.8815 (mt) cc_final: 0.8531 (mm) REVERT: C 75 MET cc_start: 0.7797 (tpp) cc_final: 0.7513 (tpp) REVERT: C 213 TYR cc_start: 0.7524 (m-80) cc_final: 0.7091 (m-80) REVERT: E 8 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7211 (pt0) REVERT: E 63 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7313 (mt-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2125 time to fit residues: 32.8991 Evaluate side-chains 84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.113215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.092848 restraints weight = 50221.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.093051 restraints weight = 37074.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.093396 restraints weight = 34565.461| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10891 Z= 0.315 Angle : 0.708 9.075 14954 Z= 0.376 Chirality : 0.047 0.208 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.262 173.333 1931 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.49 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.23), residues: 1171 helix: -0.74 (0.29), residues: 288 sheet: -1.78 (0.30), residues: 314 loop : -3.11 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP E 50 HIS 0.008 0.001 HIS B 157 PHE 0.037 0.002 PHE C 139 TYR 0.037 0.002 TYR C 59 ARG 0.004 0.001 ARG C 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9137 (t) cc_final: 0.8803 (p) REVERT: A 241 MET cc_start: 0.3598 (mtp) cc_final: 0.3360 (mtp) REVERT: B 126 ASN cc_start: 0.7631 (t0) cc_final: 0.7391 (t0) REVERT: B 136 LEU cc_start: 0.7245 (tp) cc_final: 0.7037 (tp) REVERT: B 216 GLU cc_start: 0.4965 (mm-30) cc_final: 0.4709 (mm-30) REVERT: C 1 MET cc_start: 0.6964 (tpp) cc_final: 0.6723 (tpp) REVERT: C 44 ILE cc_start: 0.8574 (mt) cc_final: 0.8344 (mm) REVERT: C 213 TYR cc_start: 0.7824 (m-80) cc_final: 0.7433 (m-80) REVERT: E 8 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7316 (pt0) REVERT: E 63 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7421 (mt-10) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2113 time to fit residues: 30.4831 Evaluate side-chains 81 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 267 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 = 0.4220 r_free = 0.4220 target = 0.112990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.095114 restraints weight = 47010.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.095937 restraints weight = 40419.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.096596 restraints weight = 32893.492| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10891 Z= 0.203 Angle : 0.619 8.484 14954 Z= 0.331 Chirality : 0.044 0.172 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.195 173.459 1931 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.02 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.24), residues: 1171 helix: -0.57 (0.30), residues: 292 sheet: -1.48 (0.31), residues: 291 loop : -3.00 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 50 HIS 0.006 0.001 HIS B 157 PHE 0.024 0.002 PHE C 139 TYR 0.028 0.001 TYR C 59 ARG 0.006 0.000 ARG C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.54 seconds wall clock time: 51 minutes 19.19 seconds (3079.19 seconds total)