Starting phenix.real_space_refine on Sun Jul 21 16:41:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzw_26920/07_2024/7uzw_26920.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzw_26920/07_2024/7uzw_26920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzw_26920/07_2024/7uzw_26920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzw_26920/07_2024/7uzw_26920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzw_26920/07_2024/7uzw_26920.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzw_26920/07_2024/7uzw_26920.cif" } resolution = 3.55 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= 0.030 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: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 32 5.16 5 C 9199 2.51 5 N 2538 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "H TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F GLU 343": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14754 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "B" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1531 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 2 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1620 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain breaks: 1 Chain: "E" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1458 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain breaks: 2 Chain: "H" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2355 Classifications: {'peptide': 293} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 3886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3886 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 5, 'TRANS': 472} Chain breaks: 6 Chain: "G" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 664 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 11, 'rna3p': 19} Time building chain proxies: 8.84, per 1000 atoms: 0.60 Number of scatterers: 14754 At special positions: 0 Unit cell: (92.4, 119.9, 203.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 31 15.00 O 2954 8.00 N 2538 7.00 C 9199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 2.4 seconds 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 21 sheets defined 39.8% alpha, 21.1% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.844A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.629A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.899A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.996A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.630A pdb=" N ARG C 187 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.689A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'E' and resid 47 through 63 removed outlier: 3.753A pdb=" N ILE E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'E' and resid 76 through 83 Processing helix chain 'E' and resid 104 through 115 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 50 through 55 removed outlier: 3.959A pdb=" N ASN H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 93 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.504A pdb=" N LEU H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 228 through 236 removed outlier: 4.446A pdb=" N GLU H 233 " --> pdb=" O LYS H 229 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER H 234 " --> pdb=" O GLU H 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.872A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 Processing helix chain 'F' and resid 25 through 29 removed outlier: 4.175A pdb=" N SER F 29 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.935A pdb=" N TYR F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.857A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 154 through 170 Processing helix chain 'F' and resid 177 through 190 Processing helix chain 'F' and resid 205 through 227 removed outlier: 3.614A pdb=" N HIS F 209 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 227 " --> pdb=" O TYR F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 245 through 249 removed outlier: 3.525A pdb=" N GLN F 248 " --> pdb=" O SER F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 279 through 300 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.784A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 386 removed outlier: 4.263A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 397 Processing helix chain 'F' and resid 423 through 437 Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 535 through 542 removed outlier: 3.680A pdb=" N THR F 539 " --> pdb=" O ASN F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 567 removed outlier: 3.634A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 574 Processing helix chain 'F' and resid 595 through 612 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.148A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER A 3 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS A 4 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR A 10 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASP A 196 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 12 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE A 194 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 14 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE A 192 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 127 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.539A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.454A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.750A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.750A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER C 3 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.190A pdb=" N VAL D 151 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA D 101 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP D 149 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE D 103 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU D 147 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 119 through 127 Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.203A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER E 8 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR E 197 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.990A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS E 4 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.893A pdb=" N ILE H 58 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 166 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 71 " --> pdb=" O PRO H 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.893A pdb=" N ILE H 58 " --> pdb=" O LYS H 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS H 166 " --> pdb=" O ILE H 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AB7, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AB8, first strand: chain 'H' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.591A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC2, first strand: chain 'F' and resid 307 through 311 removed outlier: 5.899A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.958A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 6.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4805 1.34 - 1.47: 3719 1.47 - 1.60: 6459 1.60 - 1.73: 33 1.73 - 1.85: 57 Bond restraints: 15073 Sorted by residual: bond pdb=" C1' U G 24 " pdb=" N1 U G 24 " ideal model delta sigma weight residual 1.480 1.563 -0.083 1.50e-02 4.44e+03 3.04e+01 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.41e-02 5.03e+03 5.99e+00 bond pdb=" N ARG D 137 " pdb=" CA ARG D 137 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.38e+00 bond pdb=" CB CYS F 214 " pdb=" SG CYS F 214 " ideal model delta sigma weight residual 1.808 1.738 0.070 3.30e-02 9.18e+02 4.54e+00 ... (remaining 15068 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 389 106.41 - 113.31: 8171 113.31 - 120.21: 5542 120.21 - 127.12: 6158 127.12 - 134.02: 159 Bond angle restraints: 20419 Sorted by residual: angle pdb=" O4' G G 15 " pdb=" C1' G G 15 " pdb=" N9 G G 15 " ideal model delta sigma weight residual 108.20 116.11 -7.91 1.50e+00 4.44e-01 2.78e+01 angle pdb=" N ARG F 279 " pdb=" CA ARG F 279 " pdb=" C ARG F 279 " ideal model delta sigma weight residual 114.56 108.85 5.71 1.27e+00 6.20e-01 2.02e+01 angle pdb=" C3' G G 15 " pdb=" O3' G G 15 " pdb=" P C G 16 " ideal model delta sigma weight residual 120.20 126.41 -6.21 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CB MET F 468 " pdb=" CG MET F 468 " pdb=" SD MET F 468 " ideal model delta sigma weight residual 112.70 123.16 -10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" N SER F 440 " pdb=" CA SER F 440 " pdb=" C SER F 440 " ideal model delta sigma weight residual 110.61 114.87 -4.26 1.25e+00 6.40e-01 1.16e+01 ... (remaining 20414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 8853 35.05 - 70.09: 192 70.09 - 105.14: 10 105.14 - 140.19: 2 140.19 - 175.23: 3 Dihedral angle restraints: 9060 sinusoidal: 4003 harmonic: 5057 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -3.18 -156.82 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 43.41 -171.41 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -41.40 -118.60 1 1.50e+01 4.44e-03 6.31e+01 ... (remaining 9057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1826 0.060 - 0.120: 371 0.120 - 0.181: 61 0.181 - 0.241: 7 0.241 - 0.301: 2 Chirality restraints: 2267 Sorted by residual: chirality pdb=" C1' G G 15 " pdb=" O4' G G 15 " pdb=" C2' G G 15 " pdb=" N9 G G 15 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER B 33 " pdb=" N SER B 33 " pdb=" C SER B 33 " pdb=" CB SER B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ARG D 137 " pdb=" N ARG D 137 " pdb=" C ARG D 137 " pdb=" CB ARG D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2264 not shown) Planarity restraints: 2531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 15 " 0.043 2.00e-02 2.50e+03 2.14e-02 1.38e+01 pdb=" N9 G G 15 " -0.059 2.00e-02 2.50e+03 pdb=" C8 G G 15 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G G 15 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G G 15 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G G 15 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G G 15 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G G 15 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G G 15 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G G 15 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G G 15 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G G 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 135 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 136 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 136 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 136 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 46 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 47 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 47 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 47 " 0.028 5.00e-02 4.00e+02 ... (remaining 2528 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 99 2.54 - 3.13: 11025 3.13 - 3.72: 20974 3.72 - 4.31: 29287 4.31 - 4.90: 49855 Nonbonded interactions: 111240 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.945 2.520 nonbonded pdb=" O ILE A 19 " pdb=" O2' G G 15 " model vdw 1.982 2.440 nonbonded pdb=" OG1 THR B 126 " pdb=" OD1 ASN B 135 " model vdw 2.060 2.440 nonbonded pdb=" OH TYR H 148 " pdb=" O2' A G 7 " model vdw 2.126 2.440 nonbonded pdb=" O SER F 11 " pdb=" ND1 HIS F 14 " model vdw 2.137 2.520 ... (remaining 111235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'B' and (resid 2 through 23 or resid 33 through 120 or resid 141 through \ 214)) selection = (chain 'C' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'D' and (resid 2 through 63 or resid 76 through 120 or resid 141 through \ 214)) selection = (chain 'E' and (resid 2 through 63 or resid 76 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.860 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.006 0.083 15073 Z= 0.417 Angle : 0.766 10.461 20419 Z= 0.434 Chirality : 0.050 0.301 2267 Planarity : 0.004 0.054 2531 Dihedral : 14.769 175.232 5807 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % 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: -0.88 (0.19), residues: 1718 helix: 0.56 (0.21), residues: 632 sheet: 0.13 (0.28), residues: 343 loop : -1.98 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 339 HIS 0.018 0.001 HIS D 62 PHE 0.025 0.002 PHE C 166 TYR 0.021 0.002 TYR C 206 ARG 0.020 0.001 ARG D 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 1.791 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.3350 time to fit residues: 126.3831 Evaluate side-chains 119 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 69 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN ** F 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15073 Z= 0.220 Angle : 0.640 7.146 20419 Z= 0.345 Chirality : 0.044 0.206 2267 Planarity : 0.004 0.065 2531 Dihedral : 14.005 177.346 2344 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.55 % Allowed : 8.70 % Favored : 89.75 % 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: -0.20 (0.20), residues: 1718 helix: 1.23 (0.21), residues: 646 sheet: 0.52 (0.28), residues: 345 loop : -1.78 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 52 HIS 0.017 0.001 HIS A 72 PHE 0.019 0.001 PHE E 148 TYR 0.012 0.001 TYR H 255 ARG 0.007 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.682 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 565 PHE cc_start: 0.8423 (m-80) cc_final: 0.7884 (m-80) outliers start: 24 outliers final: 13 residues processed: 152 average time/residue: 0.2958 time to fit residues: 65.1010 Evaluate side-chains 115 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 478 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 0.0020 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN C 40 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15073 Z= 0.236 Angle : 0.599 13.004 20419 Z= 0.318 Chirality : 0.043 0.328 2267 Planarity : 0.003 0.040 2531 Dihedral : 13.801 177.076 2344 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.26 % Allowed : 10.19 % Favored : 87.56 % 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: 0.07 (0.20), residues: 1718 helix: 1.48 (0.21), residues: 647 sheet: 0.84 (0.30), residues: 322 loop : -1.68 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 184 HIS 0.015 0.001 HIS A 72 PHE 0.021 0.001 PHE E 148 TYR 0.014 0.001 TYR A 180 ARG 0.004 0.000 ARG F 299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.746 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6646 (pttt) REVERT: F 1 MET cc_start: 0.5596 (mmt) cc_final: 0.5191 (mmt) REVERT: F 565 PHE cc_start: 0.8426 (m-80) cc_final: 0.7895 (m-80) outliers start: 35 outliers final: 20 residues processed: 135 average time/residue: 0.2920 time to fit residues: 57.5460 Evaluate side-chains 112 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS D 125 ASN E 110 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 493 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15073 Z= 0.492 Angle : 0.763 10.329 20419 Z= 0.406 Chirality : 0.047 0.222 2267 Planarity : 0.004 0.040 2531 Dihedral : 14.015 172.383 2344 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.90 % Allowed : 11.93 % Favored : 85.17 % 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: -0.58 (0.19), residues: 1718 helix: 0.79 (0.19), residues: 648 sheet: 0.45 (0.29), residues: 332 loop : -1.90 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 184 HIS 0.011 0.002 HIS D 62 PHE 0.026 0.002 PHE F 40 TYR 0.026 0.002 TYR A 180 ARG 0.006 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 84 time to evaluate : 1.781 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7685 (p0) REVERT: H 13 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7295 (pttt) outliers start: 45 outliers final: 26 residues processed: 120 average time/residue: 0.2834 time to fit residues: 50.6879 Evaluate side-chains 100 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS H 214 GLN H 251 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15073 Z= 0.169 Angle : 0.566 13.775 20419 Z= 0.301 Chirality : 0.042 0.179 2267 Planarity : 0.003 0.036 2531 Dihedral : 13.718 178.389 2344 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.32 % Allowed : 13.60 % Favored : 84.07 % 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: 0.04 (0.20), residues: 1718 helix: 1.56 (0.21), residues: 647 sheet: 0.67 (0.29), residues: 324 loop : -1.73 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 184 HIS 0.008 0.001 HIS D 62 PHE 0.023 0.001 PHE E 148 TYR 0.012 0.001 TYR A 180 ARG 0.003 0.000 ARG F 553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.944 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: symmetry clash REVERT: D 67 MET cc_start: 0.6408 (pmm) cc_final: 0.5892 (pmm) REVERT: H 13 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6713 (pttt) outliers start: 36 outliers final: 22 residues processed: 122 average time/residue: 0.2661 time to fit residues: 48.9888 Evaluate side-chains 97 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15073 Z= 0.203 Angle : 0.563 12.110 20419 Z= 0.296 Chirality : 0.041 0.168 2267 Planarity : 0.003 0.045 2531 Dihedral : 13.597 176.885 2344 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.19 % Allowed : 14.25 % Favored : 83.56 % 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: 0.18 (0.20), residues: 1718 helix: 1.70 (0.21), residues: 647 sheet: 0.74 (0.29), residues: 323 loop : -1.67 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 184 HIS 0.007 0.001 HIS A 72 PHE 0.022 0.001 PHE E 148 TYR 0.011 0.001 TYR F 463 ARG 0.004 0.000 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 1.829 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: symmetry clash REVERT: A 91 ILE cc_start: 0.7551 (mm) cc_final: 0.7334 (mm) REVERT: C 149 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7174 (p0) REVERT: H 13 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6942 (pttt) outliers start: 34 outliers final: 28 residues processed: 110 average time/residue: 0.2829 time to fit residues: 46.7932 Evaluate side-chains 107 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 104 optimal weight: 3.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 114 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15073 Z= 0.396 Angle : 0.676 10.804 20419 Z= 0.356 Chirality : 0.044 0.195 2267 Planarity : 0.004 0.046 2531 Dihedral : 13.758 173.787 2344 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.71 % Allowed : 15.02 % Favored : 82.27 % 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: -0.16 (0.20), residues: 1718 helix: 1.38 (0.20), residues: 645 sheet: 0.67 (0.29), residues: 321 loop : -1.88 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 184 HIS 0.009 0.001 HIS D 62 PHE 0.028 0.002 PHE E 148 TYR 0.016 0.002 TYR F 479 ARG 0.004 0.000 ARG F 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 MET cc_start: 0.6958 (tmm) cc_final: 0.6532 (tmm) REVERT: E 37 ARG cc_start: 0.8231 (mtm-85) cc_final: 0.7545 (mmt90) REVERT: H 13 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6951 (pttt) REVERT: F 278 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8732 (pp) outliers start: 42 outliers final: 32 residues processed: 110 average time/residue: 0.2764 time to fit residues: 46.0216 Evaluate side-chains 106 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15073 Z= 0.162 Angle : 0.569 12.749 20419 Z= 0.298 Chirality : 0.041 0.179 2267 Planarity : 0.003 0.042 2531 Dihedral : 13.609 177.442 2344 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.13 % Allowed : 15.28 % Favored : 82.59 % 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: 0.14 (0.20), residues: 1718 helix: 1.71 (0.21), residues: 648 sheet: 0.67 (0.29), residues: 323 loop : -1.73 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 184 HIS 0.008 0.001 HIS A 72 PHE 0.025 0.001 PHE E 148 TYR 0.010 0.001 TYR E 2 ARG 0.005 0.000 ARG F 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6923 (pttm) REVERT: H 13 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6828 (pttt) REVERT: F 41 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7701 (mt) outliers start: 33 outliers final: 22 residues processed: 111 average time/residue: 0.2522 time to fit residues: 42.9250 Evaluate side-chains 101 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15073 Z= 0.251 Angle : 0.604 13.703 20419 Z= 0.314 Chirality : 0.042 0.173 2267 Planarity : 0.003 0.042 2531 Dihedral : 13.586 175.465 2344 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.87 % Allowed : 16.05 % Favored : 82.08 % 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: 0.12 (0.20), residues: 1718 helix: 1.71 (0.21), residues: 648 sheet: 0.50 (0.28), residues: 340 loop : -1.72 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 184 HIS 0.008 0.001 HIS A 72 PHE 0.029 0.001 PHE E 148 TYR 0.034 0.001 TYR F 284 ARG 0.004 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 75 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6942 (pttt) REVERT: F 41 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7894 (tp) outliers start: 29 outliers final: 24 residues processed: 98 average time/residue: 0.2661 time to fit residues: 40.2217 Evaluate side-chains 101 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 0.0770 chunk 175 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS E 113 GLN H 17 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15073 Z= 0.164 Angle : 0.580 14.215 20419 Z= 0.298 Chirality : 0.041 0.176 2267 Planarity : 0.003 0.043 2531 Dihedral : 13.444 177.272 2344 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.87 % Allowed : 16.44 % Favored : 81.69 % 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: 0.23 (0.20), residues: 1718 helix: 1.84 (0.21), residues: 648 sheet: 0.59 (0.29), residues: 326 loop : -1.67 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 184 HIS 0.008 0.001 HIS A 72 PHE 0.027 0.001 PHE E 148 TYR 0.010 0.001 TYR F 463 ARG 0.012 0.000 ARG E 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7093 (pttm) REVERT: H 13 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6639 (pttt) REVERT: F 41 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7707 (mt) outliers start: 29 outliers final: 23 residues processed: 105 average time/residue: 0.2694 time to fit residues: 43.2605 Evaluate side-chains 103 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 77 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 103 PHE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 163 PHE Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 548 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 0.1980 chunk 58 optimal weight: 0.0370 chunk 143 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.056543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042059 restraints weight = 82328.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043459 restraints weight = 44986.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044395 restraints weight = 30794.159| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15073 Z= 0.169 Angle : 0.588 14.983 20419 Z= 0.300 Chirality : 0.042 0.214 2267 Planarity : 0.003 0.047 2531 Dihedral : 13.302 177.075 2344 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.93 % Allowed : 16.51 % Favored : 81.56 % 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: 0.26 (0.20), residues: 1718 helix: 1.86 (0.21), residues: 649 sheet: 0.63 (0.28), residues: 326 loop : -1.66 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 184 HIS 0.008 0.001 HIS A 72 PHE 0.027 0.001 PHE E 148 TYR 0.052 0.001 TYR F 284 ARG 0.011 0.000 ARG E 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2684.95 seconds wall clock time: 49 minutes 39.42 seconds (2979.42 seconds total)