Starting phenix.real_space_refine on Fri Mar 15 04:27:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/03_2024/7rpw_24624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/03_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_24624/03_2024/7rpw_24624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/03_2024/7rpw_24624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/03_2024/7rpw_24624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/03_2024/7rpw_24624_updated.pdb" } 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-5265/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: 5.95, 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 - 3.50 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: 4.72 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... running ksdssp... Secondary structure from input PDB file: 31 helices and 14 sheets defined 24.4% alpha, 15.8% beta 30 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 75 through 81 removed outlier: 4.569A pdb=" N LYS A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 202 through 211 removed outlier: 4.258A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 199 through 206 removed outlier: 4.433A pdb=" N THR B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 19 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) Processing helix chain 'C' and resid 71 through 80 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) removed outlier: 5.721A pdb=" N VAL C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 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 3 through 11 Processing helix chain 'E' and resid 19 through 32 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 38 through 46 Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 78 through 87 Processing helix chain 'E' and resid 91 through 98 removed outlier: 3.840A pdb=" N ARG E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU E 98 " --> pdb=" O VAL E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 139 through 152 Processing helix chain 'E' and resid 161 through 167 Processing helix chain 'E' and resid 176 through 188 Processing helix chain 'E' and resid 191 through 203 removed outlier: 3.656A pdb=" N GLU E 195 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE E 196 " --> pdb=" O ALA E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 291 through 299 removed outlier: 3.564A pdb=" N ASP E 294 " --> pdb=" O ASP E 291 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR E 295 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 296 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR E 299 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 332 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) removed outlier: 4.417A pdb=" N ARG E 332 " --> pdb=" O MET E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 367 through 374 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) Processing helix chain 'E' and resid 393 through 406 Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'A' and resid 66 through 71 removed outlier: 4.405A pdb=" N LEU A 28 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 70 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N SER A 25 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 40 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 27 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 38 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 35 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE A 49 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 242 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'A' and resid 157 through 160 removed outlier: 3.603A pdb=" N ALA A 179 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= E, 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= F, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= G, 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= H, first strand: chain 'B' and resid 133 through 135 Processing sheet with id= I, 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) Processing sheet with id= J, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.763A pdb=" N TYR C 5 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 87 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 97 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id= K, 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= L, first strand: chain 'C' and resid 192 through 197 removed outlier: 3.890A pdb=" N SER C 192 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 239 through 241 removed outlier: 4.088A pdb=" N GLU E 239 " --> pdb=" O TRP E 431 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 433 " --> pdb=" O GLU E 239 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 241 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing sheet with id= N, 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: 7.494A pdb=" N GLU E 308 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU E 352 " --> pdb=" O GLU E 308 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 714 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: 3.24 Time building geometry restraints manager: 5.06 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: 6139 3.01 - 3.64: 17045 3.64 - 4.27: 23672 4.27 - 4.90: 36846 Nonbonded interactions: 83764 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 83759 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 2.030 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.360 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- 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= 0.202 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 : 1.219 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: 0.2274 time to fit residues: 76.0398 Evaluate side-chains 149 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 103 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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: 0.3980 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 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: 6.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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** ** 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: 0.6776 moved from start: 0.2428 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= 0.234 Angle : 0.652 6.804 14954 Z= 0.351 Chirality : 0.046 0.191 1724 Planarity : 0.004 0.035 1681 Dihedral : 22.072 173.177 1931 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.38 % Favored : 87.53 % Rotamer: Outliers : 0.19 % Allowed : 4.26 % Favored : 95.55 % 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: -2.86 (0.24), residues: 1171 helix: -0.75 (0.29), residues: 305 sheet: -1.44 (0.31), residues: 311 loop : -2.87 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 50 HIS 0.005 0.001 HIS B 157 PHE 0.020 0.002 PHE E 53 TYR 0.020 0.002 TYR B 56 ARG 0.006 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 152 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8081 (mp0) REVERT: B 47 PHE cc_start: 0.6330 (t80) cc_final: 0.6017 (t80) REVERT: B 146 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6204 (mt-10) REVERT: B 216 GLU cc_start: 0.4473 (mm-30) cc_final: 0.4155 (mm-30) REVERT: C 1 MET cc_start: 0.7487 (tpt) cc_final: 0.7251 (tpp) REVERT: C 44 ILE cc_start: 0.8834 (mt) cc_final: 0.8592 (mm) REVERT: C 80 VAL cc_start: 0.7684 (m) cc_final: 0.7392 (m) REVERT: E 8 GLU cc_start: 0.7745 (tm-30) cc_final: 0.6777 (pt0) REVERT: E 63 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7672 (mt-10) REVERT: E 120 THR cc_start: 0.8280 (p) cc_final: 0.7601 (m) REVERT: E 133 LEU cc_start: 0.7597 (mp) cc_final: 0.7316 (mt) REVERT: E 164 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7402 (tpt170) REVERT: E 280 ARG cc_start: 0.6049 (tmt170) cc_final: 0.5781 (tpt-90) REVERT: E 328 MET cc_start: 0.8304 (mtm) cc_final: 0.8038 (tmm) REVERT: E 360 TYR cc_start: 0.6377 (m-10) cc_final: 0.6012 (t80) REVERT: E 372 LEU cc_start: 0.6553 (tp) cc_final: 0.6300 (tp) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.2502 time to fit residues: 52.2134 Evaluate side-chains 97 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 8.9990 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 30 optimal weight: 0.0470 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 0.0050 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2911 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= 0.185 Angle : 0.592 6.138 14954 Z= 0.319 Chirality : 0.044 0.158 1724 Planarity : 0.003 0.035 1681 Dihedral : 22.122 174.013 1931 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.25 % Favored : 89.67 % Rotamer: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % 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: -2.80 (0.24), residues: 1171 helix: -0.68 (0.30), residues: 305 sheet: -1.61 (0.31), residues: 309 loop : -2.70 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 50 HIS 0.002 0.001 HIS B 157 PHE 0.015 0.002 PHE E 53 TYR 0.030 0.001 TYR C 59 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 : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6145 (mt-10) REVERT: B 216 GLU cc_start: 0.3980 (mm-30) cc_final: 0.3754 (mm-30) REVERT: C 1 MET cc_start: 0.7347 (tpt) cc_final: 0.7016 (tpp) REVERT: C 14 ILE cc_start: 0.8450 (mt) cc_final: 0.8214 (tp) REVERT: C 44 ILE cc_start: 0.8869 (mt) cc_final: 0.8594 (mm) REVERT: C 79 LYS cc_start: 0.8194 (mttt) cc_final: 0.7931 (mttp) REVERT: C 80 VAL cc_start: 0.7608 (m) cc_final: 0.7290 (m) REVERT: C 140 LYS cc_start: 0.8223 (ttmt) cc_final: 0.8011 (tmtt) REVERT: C 150 THR cc_start: 0.8669 (p) cc_final: 0.8404 (t) REVERT: C 230 MET cc_start: 0.4344 (mmt) cc_final: 0.3919 (mmt) REVERT: E 8 GLU cc_start: 0.7723 (tm-30) cc_final: 0.6810 (pt0) REVERT: E 22 LEU cc_start: 0.7489 (pp) cc_final: 0.7274 (pp) REVERT: E 25 LEU cc_start: 0.9046 (mm) cc_final: 0.8836 (pp) REVERT: E 63 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7648 (mt-10) REVERT: E 120 THR cc_start: 0.7865 (p) cc_final: 0.7649 (m) REVERT: E 133 LEU cc_start: 0.7870 (mp) cc_final: 0.7538 (mt) REVERT: E 280 ARG cc_start: 0.6087 (tmt170) cc_final: 0.5816 (tpt-90) REVERT: E 328 MET cc_start: 0.8574 (mtm) cc_final: 0.8099 (tmm) REVERT: E 360 TYR cc_start: 0.5724 (m-10) cc_final: 0.5425 (t80) REVERT: E 372 LEU cc_start: 0.6592 (tp) cc_final: 0.6370 (tp) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2571 time to fit residues: 46.2962 Evaluate side-chains 98 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 0.4980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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** C 221 GLN ** 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: 0.6784 moved from start: 0.3229 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= 0.213 Angle : 0.610 6.309 14954 Z= 0.327 Chirality : 0.044 0.148 1724 Planarity : 0.003 0.030 1681 Dihedral : 22.144 173.990 1931 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.27 % Favored : 88.64 % Rotamer: Outliers : 0.19 % Allowed : 3.39 % Favored : 96.42 % 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: -2.92 (0.24), residues: 1171 helix: -0.69 (0.30), residues: 301 sheet: -1.60 (0.31), residues: 303 loop : -2.86 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 50 HIS 0.003 0.001 HIS B 157 PHE 0.018 0.002 PHE E 53 TYR 0.030 0.002 TYR A 200 ARG 0.004 0.000 ARG B 36 *********************** 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 124 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7327 (mp) cc_final: 0.6817 (mp) REVERT: B 216 GLU cc_start: 0.4308 (mm-30) cc_final: 0.3962 (mm-30) REVERT: C 44 ILE cc_start: 0.8782 (mt) cc_final: 0.8546 (mm) REVERT: C 75 MET cc_start: 0.8503 (mmt) cc_final: 0.8239 (mmt) REVERT: C 79 LYS cc_start: 0.8387 (mttt) cc_final: 0.8042 (mttp) REVERT: C 150 THR cc_start: 0.8617 (p) cc_final: 0.8400 (t) REVERT: C 230 MET cc_start: 0.4390 (mmt) cc_final: 0.3930 (mmt) REVERT: E 8 GLU cc_start: 0.7875 (tm-30) cc_final: 0.6938 (pt0) REVERT: E 63 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7659 (mt-10) REVERT: E 120 THR cc_start: 0.7810 (p) cc_final: 0.7604 (m) REVERT: E 133 LEU cc_start: 0.7738 (mp) cc_final: 0.7441 (mt) REVERT: E 183 MET cc_start: 0.8405 (pmm) cc_final: 0.8056 (pmm) REVERT: E 280 ARG cc_start: 0.6316 (tmt170) cc_final: 0.5863 (tpt-90) REVERT: E 328 MET cc_start: 0.8583 (mtm) cc_final: 0.8090 (tmm) REVERT: E 360 TYR cc_start: 0.6235 (m-10) cc_final: 0.5407 (t80) REVERT: E 372 LEU cc_start: 0.6486 (tp) cc_final: 0.6190 (tp) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.2595 time to fit residues: 44.2706 Evaluate side-chains 90 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.0050 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 overall best weight: 1.2398 ------------------------------------------------------------------------------- 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: 0.6721 moved from start: 0.3566 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= 0.167 Angle : 0.576 5.952 14954 Z= 0.308 Chirality : 0.043 0.153 1724 Planarity : 0.003 0.028 1681 Dihedral : 22.106 174.621 1931 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -2.83 (0.24), residues: 1171 helix: -0.56 (0.31), residues: 301 sheet: -1.62 (0.31), residues: 315 loop : -2.80 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 50 HIS 0.002 0.001 HIS E 269 PHE 0.016 0.001 PHE E 53 TYR 0.020 0.001 TYR C 59 ARG 0.002 0.000 ARG E 234 *********************** 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 121 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7693 (mmm) cc_final: 0.7038 (mmm) REVERT: B 36 ARG cc_start: 0.6966 (mmt180) cc_final: 0.6592 (mmt90) REVERT: B 216 GLU cc_start: 0.4137 (mm-30) cc_final: 0.3803 (mm-30) REVERT: C 44 ILE cc_start: 0.8738 (mt) cc_final: 0.8468 (mm) REVERT: C 150 THR cc_start: 0.8674 (p) cc_final: 0.8427 (t) REVERT: C 230 MET cc_start: 0.4169 (mmt) cc_final: 0.3759 (mmt) REVERT: E 8 GLU cc_start: 0.7740 (tm-30) cc_final: 0.6860 (pt0) REVERT: E 133 LEU cc_start: 0.7465 (mp) cc_final: 0.7214 (mt) REVERT: E 150 LEU cc_start: 0.8891 (mm) cc_final: 0.8665 (tp) REVERT: E 164 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7181 (tpp-160) REVERT: E 280 ARG cc_start: 0.6306 (tmt170) cc_final: 0.5910 (tpt-90) REVERT: E 328 MET cc_start: 0.8560 (mtm) cc_final: 0.8062 (tmm) REVERT: E 360 TYR cc_start: 0.5781 (m-10) cc_final: 0.5183 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2513 time to fit residues: 42.3610 Evaluate side-chains 87 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 113 optimal weight: 0.0970 overall best weight: 3.0184 ------------------------------------------------------------------------------- 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 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: 0.6852 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10891 Z= 0.268 Angle : 0.659 9.254 14954 Z= 0.349 Chirality : 0.046 0.179 1724 Planarity : 0.004 0.031 1681 Dihedral : 22.188 173.790 1931 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.81 % Favored : 87.11 % 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 : 0.00 % 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: -3.09 (0.23), residues: 1171 helix: -0.81 (0.30), residues: 293 sheet: -1.62 (0.30), residues: 327 loop : -3.05 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 50 HIS 0.005 0.001 HIS A 39 PHE 0.024 0.002 PHE C 228 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 105 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7615 (mmm) cc_final: 0.6944 (mmm) REVERT: B 36 ARG cc_start: 0.7068 (mmt180) cc_final: 0.6655 (mmt90) REVERT: B 145 ASP cc_start: 0.8537 (m-30) cc_final: 0.8282 (m-30) REVERT: B 216 GLU cc_start: 0.4438 (mm-30) cc_final: 0.4047 (mm-30) REVERT: C 44 ILE cc_start: 0.8718 (mt) cc_final: 0.8469 (mm) REVERT: C 75 MET cc_start: 0.8679 (mmt) cc_final: 0.8256 (tpp) REVERT: C 150 THR cc_start: 0.8593 (p) cc_final: 0.8343 (t) REVERT: C 230 MET cc_start: 0.4452 (mmt) cc_final: 0.3995 (mmt) REVERT: E 8 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7079 (pt0) REVERT: E 133 LEU cc_start: 0.7753 (mp) cc_final: 0.7378 (mt) REVERT: E 164 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7351 (tpp-160) REVERT: E 183 MET cc_start: 0.8404 (pmm) cc_final: 0.8101 (pmm) REVERT: E 280 ARG cc_start: 0.6389 (tmt170) cc_final: 0.5992 (tpt-90) REVERT: E 328 MET cc_start: 0.8582 (mtm) cc_final: 0.8059 (tmm) REVERT: E 360 TYR cc_start: 0.5329 (m-10) cc_final: 0.4509 (t80) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2291 time to fit residues: 34.6402 Evaluate side-chains 84 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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: 0.0020 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 391 ASN E 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3911 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= 0.155 Angle : 0.573 7.854 14954 Z= 0.305 Chirality : 0.043 0.160 1724 Planarity : 0.003 0.031 1681 Dihedral : 22.092 174.701 1931 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.94 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -0.58 (0.31), residues: 303 sheet: -1.56 (0.31), residues: 309 loop : -2.86 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 50 HIS 0.002 0.001 HIS A 39 PHE 0.014 0.001 PHE E 53 TYR 0.021 0.001 TYR C 59 ARG 0.005 0.000 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 116 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8128 (mm) cc_final: 0.7809 (tp) REVERT: A 229 MET cc_start: 0.7795 (mmm) cc_final: 0.7414 (mmm) REVERT: B 36 ARG cc_start: 0.7028 (mmt180) cc_final: 0.6250 (mmt-90) REVERT: B 129 PHE cc_start: 0.6311 (m-80) cc_final: 0.6075 (m-80) REVERT: B 216 GLU cc_start: 0.4138 (mm-30) cc_final: 0.3811 (mm-30) REVERT: C 1 MET cc_start: 0.7335 (tpp) cc_final: 0.7103 (tpp) REVERT: C 44 ILE cc_start: 0.8816 (mt) cc_final: 0.8530 (mm) REVERT: C 75 MET cc_start: 0.8254 (mmt) cc_final: 0.7757 (tpp) REVERT: C 220 ASN cc_start: 0.7811 (m-40) cc_final: 0.7404 (m-40) REVERT: E 8 GLU cc_start: 0.7815 (tm-30) cc_final: 0.6816 (pt0) REVERT: E 133 LEU cc_start: 0.7358 (mp) cc_final: 0.7026 (mt) REVERT: E 164 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7226 (tpp-160) REVERT: E 280 ARG cc_start: 0.6561 (tmt170) cc_final: 0.6122 (tpt-90) REVERT: E 328 MET cc_start: 0.8545 (mtm) cc_final: 0.8033 (tmm) REVERT: E 360 TYR cc_start: 0.4911 (m-10) cc_final: 0.4484 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2351 time to fit residues: 38.4561 Evaluate side-chains 88 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 58 optimal weight: 0.0050 chunk 10 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN E 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4033 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= 0.170 Angle : 0.575 7.760 14954 Z= 0.305 Chirality : 0.044 0.168 1724 Planarity : 0.003 0.034 1681 Dihedral : 22.059 175.169 1931 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.50 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.24), residues: 1171 helix: -0.44 (0.31), residues: 300 sheet: -1.55 (0.30), residues: 314 loop : -2.99 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 50 HIS 0.004 0.001 HIS E 387 PHE 0.016 0.001 PHE E 53 TYR 0.010 0.001 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 114 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8259 (mm) cc_final: 0.8038 (tp) REVERT: A 229 MET cc_start: 0.8062 (mmm) cc_final: 0.7773 (mmm) REVERT: B 36 ARG cc_start: 0.6961 (mmt180) cc_final: 0.6549 (mmt90) REVERT: B 216 GLU cc_start: 0.4215 (mm-30) cc_final: 0.3884 (mm-30) REVERT: C 1 MET cc_start: 0.7190 (tpp) cc_final: 0.6939 (tpp) REVERT: C 44 ILE cc_start: 0.8729 (mt) cc_final: 0.8445 (mm) REVERT: C 75 MET cc_start: 0.8170 (mmt) cc_final: 0.7615 (tpp) REVERT: C 220 ASN cc_start: 0.7805 (m-40) cc_final: 0.7238 (m-40) REVERT: E 8 GLU cc_start: 0.7818 (tm-30) cc_final: 0.6948 (pt0) REVERT: E 133 LEU cc_start: 0.7297 (mp) cc_final: 0.6892 (mt) REVERT: E 280 ARG cc_start: 0.6650 (tmt170) cc_final: 0.6260 (tpt-90) REVERT: E 328 MET cc_start: 0.8558 (mtm) cc_final: 0.8020 (tmm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2215 time to fit residues: 37.4692 Evaluate side-chains 87 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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: 9.9990 chunk 102 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4118 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= 0.181 Angle : 0.582 8.513 14954 Z= 0.310 Chirality : 0.044 0.244 1724 Planarity : 0.003 0.041 1681 Dihedral : 22.061 175.147 1931 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.67 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.24), residues: 1171 helix: -0.42 (0.31), residues: 298 sheet: -1.50 (0.30), residues: 324 loop : -2.99 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 50 HIS 0.003 0.001 HIS A 39 PHE 0.015 0.001 PHE E 53 TYR 0.009 0.001 TYR E 360 ARG 0.002 0.000 ARG B 82 *********************** 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 105 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8249 (mm) cc_final: 0.7815 (tp) REVERT: A 37 SER cc_start: 0.7430 (t) cc_final: 0.6776 (p) REVERT: A 229 MET cc_start: 0.7914 (mmm) cc_final: 0.7506 (mmm) REVERT: B 216 GLU cc_start: 0.4234 (mm-30) cc_final: 0.3859 (mm-30) REVERT: C 1 MET cc_start: 0.7233 (tpp) cc_final: 0.7008 (tpp) REVERT: C 44 ILE cc_start: 0.8721 (mt) cc_final: 0.8450 (mm) REVERT: C 75 MET cc_start: 0.8204 (mmt) cc_final: 0.7757 (tpp) REVERT: C 220 ASN cc_start: 0.7742 (m-40) cc_final: 0.7151 (m-40) REVERT: E 8 GLU cc_start: 0.7833 (tm-30) cc_final: 0.6962 (pt0) REVERT: E 133 LEU cc_start: 0.7392 (mp) cc_final: 0.7014 (mt) REVERT: E 280 ARG cc_start: 0.6702 (tmt170) cc_final: 0.6356 (tpt-90) REVERT: E 328 MET cc_start: 0.8561 (mtm) cc_final: 0.8023 (tmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2262 time to fit residues: 34.2705 Evaluate side-chains 83 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 0.0770 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10891 Z= 0.247 Angle : 0.645 9.073 14954 Z= 0.343 Chirality : 0.045 0.170 1724 Planarity : 0.004 0.041 1681 Dihedral : 22.143 174.138 1931 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.13 % Favored : 87.79 % 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: -3.05 (0.24), residues: 1171 helix: -0.79 (0.30), residues: 300 sheet: -1.63 (0.30), residues: 325 loop : -3.02 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 50 HIS 0.004 0.001 HIS A 39 PHE 0.022 0.002 PHE C 228 TYR 0.013 0.002 TYR C 59 ARG 0.004 0.001 ARG E 234 ********************** 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 102 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7678 (mmm) cc_final: 0.6994 (mmm) REVERT: A 241 MET cc_start: 0.3956 (mtp) cc_final: 0.3626 (mtp) REVERT: B 36 ARG cc_start: 0.7009 (mpt180) cc_final: 0.6736 (mpt180) REVERT: B 129 PHE cc_start: 0.6078 (m-80) cc_final: 0.5838 (m-80) REVERT: B 216 GLU cc_start: 0.4403 (mm-30) cc_final: 0.4133 (mm-30) REVERT: C 1 MET cc_start: 0.7169 (tpp) cc_final: 0.6890 (tpp) REVERT: C 44 ILE cc_start: 0.8690 (mt) cc_final: 0.8435 (mm) REVERT: C 75 MET cc_start: 0.8462 (mmt) cc_final: 0.7964 (tpp) REVERT: C 220 ASN cc_start: 0.7604 (m-40) cc_final: 0.7327 (m-40) REVERT: E 8 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7081 (pt0) REVERT: E 63 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7523 (mt-10) REVERT: E 133 LEU cc_start: 0.7354 (mp) cc_final: 0.7104 (mt) REVERT: E 280 ARG cc_start: 0.6612 (tmt170) cc_final: 0.6323 (tpt-90) REVERT: E 328 MET cc_start: 0.8577 (mtm) cc_final: 0.8010 (tmm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2278 time to fit residues: 33.6685 Evaluate side-chains 79 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 4.9990 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** 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 = 0.4187 r_free = 0.4187 target = 0.111322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.093721 restraints weight = 47168.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.094829 restraints weight = 40555.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.095148 restraints weight = 34547.537| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3863 r_free = 0.3863 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4261 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= 0.248 Angle : 0.646 8.995 14954 Z= 0.344 Chirality : 0.045 0.232 1724 Planarity : 0.004 0.042 1681 Dihedral : 22.190 173.214 1931 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.47 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: -3.23 (0.23), residues: 1171 helix: -1.04 (0.29), residues: 302 sheet: -1.68 (0.29), residues: 339 loop : -3.13 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 50 HIS 0.004 0.001 HIS B 157 PHE 0.020 0.002 PHE C 228 TYR 0.013 0.002 TYR B 56 ARG 0.005 0.001 ARG E 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.42 seconds wall clock time: 35 minutes 39.48 seconds (2139.48 seconds total)