Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 20:43:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/04_2023/7rpw_24624_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/04_2023/7rpw_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_24624/04_2023/7rpw_24624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/04_2023/7rpw_24624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/04_2023/7rpw_24624_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpw_24624/04_2023/7rpw_24624_updated.pdb" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.08, per 1000 atoms: 0.57 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: 5.48 Conformation dependent library (CDL) restraints added in 1.4 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: 3.63 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: 3.57 Time building geometry restraints manager: 5.39 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: 6022 34.68 - 69.36: 377 69.36 - 104.04: 5 104.04 - 138.72: 0 138.72 - 173.39: 5 Dihedral angle restraints: 6409 sinusoidal: 2977 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 6406 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: 0.010 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: 2.500 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.040 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- 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 : 19.186 173.395 4191 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 % 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 *********************** 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 : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 40 residues processed: 239 average time/residue: 0.2382 time to fit residues: 79.4524 Evaluate side-chains 139 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 1.237 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 1 residues processed: 40 average time/residue: 0.1236 time to fit residues: 9.7690 ------------------------------------------------------------------------------- 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: 0.6980 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2483 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= 0.180 Angle : 0.600 6.532 14954 Z= 0.323 Chirality : 0.044 0.196 1724 Planarity : 0.004 0.034 1681 Dihedral : 21.906 173.764 1879 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.67 % Favored : 89.24 % Rotamer Outliers : 0.10 % 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: -2.66 (0.24), residues: 1171 helix: -0.44 (0.30), residues: 306 sheet: -1.38 (0.31), residues: 303 loop : -2.79 (0.24), residues: 562 *********************** 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 158 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2539 time to fit residues: 55.2535 Evaluate side-chains 88 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6400 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 0.0170 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- 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: 0.6874 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10891 Z= 0.306 Angle : 0.703 8.916 14954 Z= 0.374 Chirality : 0.047 0.231 1724 Planarity : 0.004 0.035 1681 Dihedral : 22.112 172.335 1879 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.49 % Favored : 86.42 % Rotamer Outliers : 0.19 % 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: -3.13 (0.23), residues: 1171 helix: -0.88 (0.29), residues: 300 sheet: -1.71 (0.30), residues: 307 loop : -3.00 (0.23), residues: 564 *********************** 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 108 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.371 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.2543 time to fit residues: 38.8359 Evaluate side-chains 73 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1068 time to fit residues: 1.9429 ------------------------------------------------------------------------------- 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: 0.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 288 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 10891 Z= 0.331 Angle : 0.727 8.295 14954 Z= 0.388 Chirality : 0.047 0.167 1724 Planarity : 0.004 0.037 1681 Dihedral : 22.295 171.407 1879 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 26.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.32 % Favored : 86.59 % Rotamer Outliers : 0.10 % 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: -3.44 (0.23), residues: 1171 helix: -1.12 (0.29), residues: 296 sheet: -1.97 (0.29), residues: 319 loop : -3.16 (0.23), residues: 556 *********************** 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 101 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.2450 time to fit residues: 35.5337 Evaluate side-chains 75 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6268 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 0.0060 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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** C 221 GLN E 391 ASN E 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3710 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= 0.193 Angle : 0.623 7.461 14954 Z= 0.333 Chirality : 0.045 0.155 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.180 172.914 1879 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.27 % Favored : 88.64 % Rotamer Outliers : 0.10 % 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: -3.21 (0.24), residues: 1171 helix: -0.92 (0.30), residues: 298 sheet: -1.84 (0.30), residues: 319 loop : -3.02 (0.23), residues: 554 *********************** 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 112 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2559 time to fit residues: 40.9053 Evaluate side-chains 82 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7119 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 157 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10891 Z= 0.218 Angle : 0.630 7.368 14954 Z= 0.335 Chirality : 0.045 0.173 1724 Planarity : 0.004 0.035 1681 Dihedral : 22.142 173.128 1879 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.21 % Favored : 87.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.23), residues: 1171 helix: -0.95 (0.30), residues: 306 sheet: -1.80 (0.30), residues: 317 loop : -3.10 (0.23), residues: 548 *********************** 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 98 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2046 time to fit residues: 30.2915 Evaluate side-chains 74 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6869 ------------------------------------------------------------------------------- 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: 20.0000 chunk 67 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 overall best weight: 2.8524 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.4027 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= 0.262 Angle : 0.660 8.174 14954 Z= 0.352 Chirality : 0.046 0.162 1724 Planarity : 0.004 0.066 1681 Dihedral : 22.196 172.765 1879 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.32 % Favored : 86.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 1171 helix: -0.92 (0.30), residues: 298 sheet: -1.92 (0.29), residues: 325 loop : -3.18 (0.23), residues: 548 *********************** 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 94 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2208 time to fit residues: 31.0599 Evaluate side-chains 73 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6800 ------------------------------------------------------------------------------- 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: 4.9990 chunk 70 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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: 0.6903 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 10891 Z= 0.302 Angle : 0.702 9.734 14954 Z= 0.375 Chirality : 0.047 0.168 1724 Planarity : 0.004 0.039 1681 Dihedral : 22.270 172.222 1879 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 24.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.75 % Favored : 86.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.23), residues: 1171 helix: -1.17 (0.29), residues: 296 sheet: -2.06 (0.29), residues: 316 loop : -3.12 (0.23), residues: 559 *********************** 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 90 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2177 time to fit residues: 29.3482 Evaluate side-chains 69 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6206 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 0.0980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.6802 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10891 Z= 0.203 Angle : 0.629 8.378 14954 Z= 0.336 Chirality : 0.045 0.174 1724 Planarity : 0.004 0.083 1681 Dihedral : 22.181 172.795 1879 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.19 % Favored : 88.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.23), residues: 1171 helix: -0.91 (0.30), residues: 304 sheet: -1.89 (0.30), residues: 305 loop : -3.05 (0.23), residues: 562 *********************** 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 : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2169 time to fit residues: 32.7449 Evaluate side-chains 77 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6485 ------------------------------------------------------------------------------- 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: 4.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 0.1980 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 10891 Z= 0.275 Angle : 0.682 9.128 14954 Z= 0.362 Chirality : 0.046 0.165 1724 Planarity : 0.005 0.074 1681 Dihedral : 22.236 172.784 1879 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.92 % Favored : 85.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.23), residues: 1171 helix: -1.02 (0.30), residues: 297 sheet: -1.99 (0.29), residues: 320 loop : -3.14 (0.24), residues: 554 ********************** 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 : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2377 time to fit residues: 33.8174 Evaluate side-chains 73 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5086 ------------------------------------------------------------------------------- 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: 9.9990 chunk 89 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 GLN E 288 GLN E 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.116452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.098999 restraints weight = 46244.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.099534 restraints weight = 37451.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.100162 restraints weight = 35201.215| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3972 r_free = 0.3972 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4796 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= 0.159 Angle : 0.595 8.316 14954 Z= 0.317 Chirality : 0.044 0.171 1724 Planarity : 0.004 0.070 1681 Dihedral : 22.060 173.669 1879 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.23), residues: 1171 helix: -0.79 (0.30), residues: 302 sheet: -1.73 (0.31), residues: 292 loop : -2.92 (0.23), residues: 577 =============================================================================== Job complete usr+sys time: 1885.38 seconds wall clock time: 35 minutes 38.65 seconds (2138.65 seconds total)