Starting phenix.real_space_refine on Sat Jul 20 11:08:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/07_2024/7rpw_24624_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/07_2024/7rpw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/07_2024/7rpw_24624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/07_2024/7rpw_24624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/07_2024/7rpw_24624_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/07_2024/7rpw_24624_neut.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 Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.30, per 1000 atoms: 0.59 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 - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 1.8 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: 3.89 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: 3.65 Time building geometry restraints manager: 5.75 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: 98.35 - 105.94: 488 105.94 - 113.54: 6205 113.54 - 121.13: 5262 121.13 - 128.73: 2931 128.73 - 136.32: 68 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 2.440 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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.010 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 103 poor density : 153 time to evaluate : 1.037 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: 0.2270 time to fit residues: 76.3338 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 0.0770 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 240 HIS ** E 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10891 Z= 0.235 Angle : 0.653 6.498 14954 Z= 0.353 Chirality : 0.046 0.228 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.076 173.275 1931 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.04 % Favored : 87.87 % Rotamer: Outliers : 0.19 % Allowed : 4.55 % 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: -2.76 (0.24), residues: 1171 helix: -0.55 (0.30), residues: 300 sheet: -1.55 (0.32), residues: 306 loop : -2.73 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 50 HIS 0.005 0.001 HIS B 157 PHE 0.023 0.002 PHE E 53 TYR 0.018 0.002 TYR B 56 ARG 0.007 0.001 ARG C 107 *********************** 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 153 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9047 (t) cc_final: 0.8817 (p) REVERT: B 146 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5831 (mt-10) REVERT: B 216 GLU cc_start: 0.4469 (mm-30) cc_final: 0.4143 (mm-30) REVERT: C 1 MET cc_start: 0.7469 (tpt) cc_final: 0.7132 (tpp) REVERT: C 44 ILE cc_start: 0.8845 (mt) cc_final: 0.8598 (mm) REVERT: C 79 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7822 (mttp) REVERT: C 80 VAL cc_start: 0.7671 (m) cc_final: 0.7384 (m) REVERT: E 8 GLU cc_start: 0.7739 (tm-30) cc_final: 0.6795 (pt0) REVERT: E 63 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7700 (mt-10) REVERT: E 133 LEU cc_start: 0.7598 (mp) cc_final: 0.7335 (mt) REVERT: E 280 ARG cc_start: 0.6174 (tmt170) cc_final: 0.5908 (tpt-90) REVERT: E 328 MET cc_start: 0.8384 (mtm) cc_final: 0.8127 (tmm) REVERT: E 360 TYR cc_start: 0.6216 (m-10) cc_final: 0.5878 (t80) REVERT: E 372 LEU cc_start: 0.6489 (tp) cc_final: 0.6212 (tp) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.2388 time to fit residues: 50.3846 Evaluate side-chains 97 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 92 optimal weight: 0.0570 chunk 75 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 37 optimal weight: 0.0050 chunk 89 optimal weight: 0.0030 chunk 109 optimal weight: 9.9990 overall best weight: 0.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10891 Z= 0.173 Angle : 0.587 6.466 14954 Z= 0.317 Chirality : 0.044 0.161 1724 Planarity : 0.003 0.035 1681 Dihedral : 22.098 174.626 1931 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.63 % Favored : 91.29 % Rotamer: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % 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: -2.61 (0.24), residues: 1171 helix: -0.32 (0.30), residues: 304 sheet: -1.66 (0.30), residues: 318 loop : -2.60 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 50 HIS 0.002 0.001 HIS E 269 PHE 0.015 0.002 PHE E 53 TYR 0.028 0.001 TYR A 200 ARG 0.003 0.000 ARG E 145 *********************** 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 133 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 GLU cc_start: 0.6499 (mt-10) cc_final: 0.5971 (mt-10) REVERT: C 1 MET cc_start: 0.7294 (tpt) cc_final: 0.6871 (tpp) REVERT: C 14 ILE cc_start: 0.8574 (mt) cc_final: 0.8316 (tp) REVERT: C 44 ILE cc_start: 0.8843 (mt) cc_final: 0.8578 (mm) REVERT: C 140 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8077 (tmtt) REVERT: C 150 THR cc_start: 0.8642 (p) cc_final: 0.8365 (t) REVERT: C 230 MET cc_start: 0.4108 (mmt) cc_final: 0.3817 (mmt) REVERT: E 8 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6787 (pt0) REVERT: E 22 LEU cc_start: 0.7584 (pp) cc_final: 0.7296 (pp) REVERT: E 63 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 133 LEU cc_start: 0.7615 (mp) cc_final: 0.7303 (mt) REVERT: E 280 ARG cc_start: 0.6071 (tmt170) cc_final: 0.5773 (tpt-90) REVERT: E 328 MET cc_start: 0.8248 (mtm) cc_final: 0.8044 (tmm) REVERT: E 360 TYR cc_start: 0.5937 (m-10) cc_final: 0.5618 (t80) REVERT: E 372 LEU cc_start: 0.6458 (tp) cc_final: 0.6242 (tp) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2380 time to fit residues: 43.7615 Evaluate side-chains 94 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.0010 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 0.0870 chunk 117 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.8566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 GLN E 202 ASN ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.3491 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= 0.158 Angle : 0.563 7.041 14954 Z= 0.302 Chirality : 0.043 0.151 1724 Planarity : 0.003 0.026 1681 Dihedral : 22.049 175.161 1931 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.97 % Favored : 90.95 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.81 % 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: -2.49 (0.24), residues: 1171 helix: -0.11 (0.30), residues: 302 sheet: -1.55 (0.31), residues: 305 loop : -2.60 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 50 HIS 0.003 0.001 HIS E 386 PHE 0.017 0.001 PHE E 53 TYR 0.019 0.001 TYR C 59 ARG 0.005 0.000 ARG C 20 *********************** 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 127 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 SER cc_start: 0.7447 (t) cc_final: 0.6989 (p) REVERT: B 216 GLU cc_start: 0.4103 (mm-30) cc_final: 0.3753 (mm-30) REVERT: C 44 ILE cc_start: 0.8857 (mt) cc_final: 0.8550 (mm) REVERT: C 65 PHE cc_start: 0.8407 (t80) cc_final: 0.8062 (t80) REVERT: C 75 MET cc_start: 0.8181 (mmp) cc_final: 0.7928 (tpp) REVERT: C 150 THR cc_start: 0.8574 (p) cc_final: 0.8343 (t) REVERT: E 8 GLU cc_start: 0.7642 (tm-30) cc_final: 0.6806 (pt0) REVERT: E 63 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7609 (mt-10) REVERT: E 133 LEU cc_start: 0.7514 (mp) cc_final: 0.7230 (mt) REVERT: E 142 LEU cc_start: 0.7642 (mp) cc_final: 0.7361 (tt) REVERT: E 150 LEU cc_start: 0.8881 (mm) cc_final: 0.8654 (tp) REVERT: E 280 ARG cc_start: 0.5923 (tmt170) cc_final: 0.5719 (tpt-90) REVERT: E 328 MET cc_start: 0.8273 (mtm) cc_final: 0.8039 (tmm) REVERT: E 360 TYR cc_start: 0.5660 (m-10) cc_final: 0.5399 (t80) REVERT: E 372 LEU cc_start: 0.6447 (tp) cc_final: 0.6232 (tp) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2617 time to fit residues: 46.2323 Evaluate side-chains 92 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.0170 overall best weight: 1.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN B 155 ASN ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3738 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= 0.167 Angle : 0.568 6.606 14954 Z= 0.303 Chirality : 0.043 0.155 1724 Planarity : 0.003 0.026 1681 Dihedral : 22.030 175.521 1931 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -2.48 (0.24), residues: 1171 helix: -0.01 (0.31), residues: 297 sheet: -1.45 (0.31), residues: 309 loop : -2.71 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 50 HIS 0.002 0.001 HIS E 386 PHE 0.017 0.001 PHE E 53 TYR 0.017 0.001 TYR C 59 ARG 0.005 0.000 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 120 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 ASN cc_start: 0.6706 (t0) cc_final: 0.6435 (m-40) REVERT: B 216 GLU cc_start: 0.4136 (mm-30) cc_final: 0.3906 (mm-30) REVERT: C 44 ILE cc_start: 0.8813 (mt) cc_final: 0.8512 (mm) REVERT: C 65 PHE cc_start: 0.8406 (t80) cc_final: 0.8089 (t80) REVERT: C 75 MET cc_start: 0.8260 (mmp) cc_final: 0.7907 (tpp) REVERT: E 8 GLU cc_start: 0.7610 (tm-30) cc_final: 0.6759 (pt0) REVERT: E 22 LEU cc_start: 0.7592 (pp) cc_final: 0.7391 (pp) REVERT: E 63 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7700 (mt-10) REVERT: E 123 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7149 (mm-30) REVERT: E 150 LEU cc_start: 0.8935 (mm) cc_final: 0.8649 (tp) REVERT: E 328 MET cc_start: 0.8295 (mtm) cc_final: 0.8025 (tmm) REVERT: E 360 TYR cc_start: 0.5959 (m-10) cc_final: 0.5318 (t80) REVERT: E 372 LEU cc_start: 0.6451 (tp) cc_final: 0.6237 (tp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2334 time to fit residues: 39.5533 Evaluate side-chains 87 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10891 Z= 0.328 Angle : 0.706 8.585 14954 Z= 0.374 Chirality : 0.047 0.171 1724 Planarity : 0.004 0.031 1681 Dihedral : 22.207 173.416 1931 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.58 % Favored : 86.34 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -2.90 (0.24), residues: 1171 helix: -0.50 (0.30), residues: 294 sheet: -1.54 (0.31), residues: 316 loop : -3.00 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP E 50 HIS 0.005 0.001 HIS B 157 PHE 0.026 0.002 PHE E 165 TYR 0.030 0.002 TYR C 59 ARG 0.005 0.001 ARG C 20 *********************** 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 103 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: 0.7522 (tp) cc_final: 0.7260 (tp) REVERT: B 145 ASP cc_start: 0.8628 (m-30) cc_final: 0.8326 (m-30) REVERT: B 216 GLU cc_start: 0.4378 (mm-30) cc_final: 0.4030 (mm-30) REVERT: C 44 ILE cc_start: 0.8684 (mt) cc_final: 0.8445 (mm) REVERT: E 8 GLU cc_start: 0.7799 (tm-30) cc_final: 0.6897 (pt0) REVERT: E 63 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7550 (mt-10) REVERT: E 133 LEU cc_start: 0.7655 (mp) cc_final: 0.7367 (mt) REVERT: E 328 MET cc_start: 0.8598 (mtm) cc_final: 0.8090 (tmm) REVERT: E 360 TYR cc_start: 0.5124 (m-10) cc_final: 0.4241 (t80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2194 time to fit residues: 32.8555 Evaluate side-chains 81 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.0870 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3915 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= 0.245 Angle : 0.641 6.922 14954 Z= 0.343 Chirality : 0.045 0.145 1724 Planarity : 0.004 0.032 1681 Dihedral : 22.212 173.543 1931 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.53 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.24), residues: 1171 helix: -0.45 (0.30), residues: 295 sheet: -1.53 (0.30), residues: 310 loop : -3.01 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 50 HIS 0.005 0.001 HIS A 39 PHE 0.020 0.002 PHE C 228 TYR 0.026 0.002 TYR C 59 ARG 0.002 0.000 ARG B 17 *********************** 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 102 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7049 (mmt180) cc_final: 0.6699 (mmt180) REVERT: B 129 PHE cc_start: 0.6319 (m-80) cc_final: 0.6017 (m-80) REVERT: B 136 LEU cc_start: 0.7513 (tp) cc_final: 0.7146 (tp) REVERT: B 145 ASP cc_start: 0.8607 (m-30) cc_final: 0.8309 (m-30) REVERT: B 216 GLU cc_start: 0.4459 (mm-30) cc_final: 0.4132 (mm-30) REVERT: C 44 ILE cc_start: 0.8720 (mt) cc_final: 0.8474 (mm) REVERT: C 150 THR cc_start: 0.8553 (p) cc_final: 0.8327 (t) REVERT: E 8 GLU cc_start: 0.7789 (tm-30) cc_final: 0.6886 (pt0) REVERT: E 25 LEU cc_start: 0.9104 (mm) cc_final: 0.8833 (pp) REVERT: E 63 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7502 (mt-10) REVERT: E 133 LEU cc_start: 0.7723 (mp) cc_final: 0.7473 (mt) REVERT: E 328 MET cc_start: 0.8518 (mtm) cc_final: 0.8005 (tmm) REVERT: E 372 LEU cc_start: 0.6355 (tp) cc_final: 0.6006 (tp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2207 time to fit residues: 33.0497 Evaluate side-chains 81 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4062 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= 0.191 Angle : 0.598 8.167 14954 Z= 0.320 Chirality : 0.044 0.192 1724 Planarity : 0.003 0.032 1681 Dihedral : 22.131 174.151 1931 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.61 % Favored : 88.30 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -2.75 (0.24), residues: 1171 helix: -0.27 (0.30), residues: 299 sheet: -1.49 (0.30), residues: 311 loop : -2.95 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 50 HIS 0.005 0.001 HIS E 387 PHE 0.021 0.002 PHE C 228 TYR 0.023 0.001 TYR C 59 ARG 0.006 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 101 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.6997 (mmt180) cc_final: 0.6620 (mmt180) REVERT: B 129 PHE cc_start: 0.6502 (m-80) cc_final: 0.6214 (m-80) REVERT: B 136 LEU cc_start: 0.7250 (tp) cc_final: 0.7035 (tp) REVERT: B 145 ASP cc_start: 0.8468 (m-30) cc_final: 0.8213 (m-30) REVERT: B 216 GLU cc_start: 0.4345 (mm-30) cc_final: 0.3976 (mm-30) REVERT: C 44 ILE cc_start: 0.8769 (mt) cc_final: 0.8511 (mm) REVERT: E 8 GLU cc_start: 0.7730 (tm-30) cc_final: 0.6870 (pt0) REVERT: E 25 LEU cc_start: 0.9072 (mm) cc_final: 0.8841 (pp) REVERT: E 133 LEU cc_start: 0.7668 (mp) cc_final: 0.7380 (mt) REVERT: E 328 MET cc_start: 0.8498 (mtm) cc_final: 0.7976 (tmm) REVERT: E 372 LEU cc_start: 0.6291 (tp) cc_final: 0.5910 (tp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2242 time to fit residues: 32.7872 Evaluate side-chains 83 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 10.0000 chunk 102 optimal weight: 0.1980 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10891 Z= 0.276 Angle : 0.670 8.181 14954 Z= 0.356 Chirality : 0.046 0.175 1724 Planarity : 0.004 0.033 1681 Dihedral : 22.182 173.584 1931 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.81 % Favored : 87.11 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.24), residues: 1171 helix: -0.51 (0.30), residues: 296 sheet: -1.69 (0.29), residues: 316 loop : -3.04 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 50 HIS 0.009 0.001 HIS B 157 PHE 0.025 0.002 PHE C 228 TYR 0.031 0.002 TYR C 59 ARG 0.006 0.001 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 100 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7732 (mmp) cc_final: 0.7419 (tpp) REVERT: B 129 PHE cc_start: 0.6254 (m-80) cc_final: 0.5977 (m-80) REVERT: B 136 LEU cc_start: 0.7474 (tp) cc_final: 0.7221 (tp) REVERT: B 145 ASP cc_start: 0.8595 (m-30) cc_final: 0.8324 (m-30) REVERT: B 215 MET cc_start: 0.6390 (ptm) cc_final: 0.5503 (ptm) REVERT: B 216 GLU cc_start: 0.4337 (mm-30) cc_final: 0.3902 (mm-30) REVERT: C 44 ILE cc_start: 0.8679 (mt) cc_final: 0.8444 (mm) REVERT: C 213 TYR cc_start: 0.7903 (m-80) cc_final: 0.7528 (m-80) REVERT: E 8 GLU cc_start: 0.7790 (tm-30) cc_final: 0.6925 (pt0) REVERT: E 133 LEU cc_start: 0.7538 (mp) cc_final: 0.7188 (mt) REVERT: E 328 MET cc_start: 0.8520 (mtm) cc_final: 0.7977 (tmm) REVERT: E 372 LEU cc_start: 0.6351 (tp) cc_final: 0.5974 (tp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2242 time to fit residues: 33.0032 Evaluate side-chains 80 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10891 Z= 0.351 Angle : 0.756 8.521 14954 Z= 0.404 Chirality : 0.048 0.235 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.348 172.281 1931 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.35 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -3.40 (0.23), residues: 1171 helix: -0.99 (0.29), residues: 294 sheet: -1.91 (0.29), residues: 318 loop : -3.21 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 50 HIS 0.015 0.002 HIS B 157 PHE 0.029 0.003 PHE C 228 TYR 0.040 0.003 TYR C 59 ARG 0.006 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 95 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: B 136 LEU cc_start: 0.7489 (tp) cc_final: 0.7122 (tp) REVERT: B 145 ASP cc_start: 0.8543 (m-30) cc_final: 0.8275 (m-30) REVERT: B 215 MET cc_start: 0.6396 (ptm) cc_final: 0.5646 (ptm) REVERT: B 216 GLU cc_start: 0.4530 (mm-30) cc_final: 0.4303 (mm-30) REVERT: C 1 MET cc_start: 0.7198 (tpp) cc_final: 0.6921 (tpp) REVERT: C 213 TYR cc_start: 0.7993 (m-80) cc_final: 0.7617 (m-80) REVERT: E 8 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7130 (pt0) REVERT: E 133 LEU cc_start: 0.7877 (mp) cc_final: 0.7542 (mt) REVERT: E 325 GLN cc_start: 0.8170 (mm110) cc_final: 0.7912 (pp30) REVERT: E 328 MET cc_start: 0.8550 (mtm) cc_final: 0.7880 (tmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2155 time to fit residues: 29.9727 Evaluate side-chains 75 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.113904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.096793 restraints weight = 47205.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.097901 restraints weight = 39567.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.098118 restraints weight = 36094.305| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4581 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= 0.179 Angle : 0.611 7.492 14954 Z= 0.325 Chirality : 0.044 0.200 1724 Planarity : 0.004 0.033 1681 Dihedral : 22.195 173.328 1931 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -2.95 (0.23), residues: 1171 helix: -0.44 (0.30), residues: 293 sheet: -1.63 (0.30), residues: 294 loop : -3.02 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 50 HIS 0.004 0.001 HIS E 269 PHE 0.018 0.001 PHE C 228 TYR 0.022 0.001 TYR C 59 ARG 0.011 0.001 ARG E 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.78 seconds wall clock time: 36 minutes 19.05 seconds (2179.05 seconds total)