Starting phenix.real_space_refine on Tue Apr 9 00:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzx_26921/04_2024/7uzx_26921.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzx_26921/04_2024/7uzx_26921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzx_26921/04_2024/7uzx_26921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzx_26921/04_2024/7uzx_26921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzx_26921/04_2024/7uzx_26921.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzx_26921/04_2024/7uzx_26921.pdb" } resolution = 3.49 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= 0.029 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 36 5.49 5 S 32 5.16 5 C 9246 2.51 5 N 2552 2.21 5 O 2992 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-5288/modules/chem_data/mon_lib" Total number of atoms: 14858 Number of models: 1 Model: "" Number of chains: 9 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: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 659 Classifications: {'RNA': 31} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 11, 'rna3p': 19} Chain: "L" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 109 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Time building chain proxies: 8.10, per 1000 atoms: 0.55 Number of scatterers: 14858 At special positions: 0 Unit cell: (92.4, 116.6, 204.6, 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 36 15.00 O 2992 8.00 N 2552 7.00 C 9246 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: 5.88 Conformation dependent library (CDL) restraints added in 2.5 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 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 4.25 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: 3.606A 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: 3.630A 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: 3.687A 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: 3.631A 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: 3.943A 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: 3.754A 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: 3.961A 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: 3.503A 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: 4.176A 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: 3.934A 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: 3.613A 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: 3.524A 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: 3.633A 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: 4.807A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.297A 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: 6.675A pdb=" N GLU A 12 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE A 194 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 5.926A 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: 4.453A 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: 6.680A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.671A 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: 3.751A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.751A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.598A 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: 6.363A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.393A 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: 7.655A 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: 7.577A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.583A 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: 4.202A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.641A 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: 4.202A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS E 6 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR E 201 " --> pdb=" O LYS E 6 " (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: 5.900A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 7.202A 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) 637 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 6.26 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: 4777 1.34 - 1.47: 3798 1.47 - 1.60: 6519 1.60 - 1.72: 36 1.72 - 1.85: 58 Bond restraints: 15188 Sorted by residual: bond pdb=" O3' G G 20 " pdb=" P U G 21 " ideal model delta sigma weight residual 1.607 1.737 -0.130 1.50e-02 4.44e+03 7.52e+01 bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.475 1.384 0.091 1.50e-02 4.44e+03 3.70e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.470 1.555 -0.085 1.50e-02 4.44e+03 3.20e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.470 1.549 -0.079 1.50e-02 4.44e+03 2.78e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.475 1.401 0.074 1.50e-02 4.44e+03 2.42e+01 ... (remaining 15183 not shown) Histogram of bond angle deviations from ideal: 51.78 - 68.23: 1 68.23 - 84.68: 0 84.68 - 101.13: 31 101.13 - 117.58: 11289 117.58 - 134.03: 9274 Bond angle restraints: 20595 Sorted by residual: angle pdb=" O3' G G 20 " pdb=" P U G 21 " pdb=" OP2 U G 21 " ideal model delta sigma weight residual 108.00 51.78 56.22 3.00e+00 1.11e-01 3.51e+02 angle pdb=" O3' G G 20 " pdb=" P U G 21 " pdb=" O5' U G 21 " ideal model delta sigma weight residual 104.00 123.70 -19.70 1.50e+00 4.44e-01 1.72e+02 angle pdb=" O3' U G 15 " pdb=" C3' U G 15 " pdb=" C2' U G 15 " ideal model delta sigma weight residual 109.50 121.01 -11.51 1.50e+00 4.44e-01 5.89e+01 angle pdb=" O3' G G 20 " pdb=" P U G 21 " pdb=" OP1 U G 21 " ideal model delta sigma weight residual 108.00 128.78 -20.78 3.00e+00 1.11e-01 4.80e+01 angle pdb=" C3' G G 20 " pdb=" O3' G G 20 " pdb=" P U G 21 " ideal model delta sigma weight residual 120.20 129.98 -9.78 1.50e+00 4.44e-01 4.25e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 8905 34.68 - 69.37: 211 69.37 - 104.05: 8 104.05 - 138.74: 2 138.74 - 173.42: 3 Dihedral angle restraints: 9129 sinusoidal: 4072 harmonic: 5057 Sorted by residual: 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 43.39 -171.39 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 -41.41 -118.59 1 1.50e+01 4.44e-03 6.31e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -147.96 61.96 1 1.00e+01 1.00e-02 5.09e+01 ... (remaining 9126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2066 0.086 - 0.171: 212 0.171 - 0.257: 13 0.257 - 0.342: 0 0.342 - 0.427: 1 Chirality restraints: 2292 Sorted by residual: chirality pdb=" C3' U G 15 " pdb=" C4' U G 15 " pdb=" O3' U G 15 " pdb=" C2' U G 15 " both_signs ideal model delta sigma weight residual False -2.74 -2.32 -0.43 2.00e-01 2.50e+01 4.57e+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 1.58e+00 chirality pdb=" P A G 14 " pdb=" OP1 A G 14 " pdb=" OP2 A G 14 " pdb=" O5' A G 14 " both_signs ideal model delta sigma weight residual True 2.41 -2.17 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2289 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 252 " 0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C PHE F 252 " -0.094 2.00e-02 2.50e+03 pdb=" O PHE F 252 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU F 253 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 15 " -0.028 2.00e-02 2.50e+03 2.52e-02 1.43e+01 pdb=" N1 U G 15 " 0.066 2.00e-02 2.50e+03 pdb=" C2 U G 15 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U G 15 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U G 15 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U G 15 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U G 15 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U G 15 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U G 15 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 134 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA A 134 " -0.061 2.00e-02 2.50e+03 pdb=" O ALA A 134 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 135 " 0.021 2.00e-02 2.50e+03 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 69 2.47 - 3.08: 10025 3.08 - 3.69: 20694 3.69 - 4.29: 30370 4.29 - 4.90: 51197 Nonbonded interactions: 112355 Sorted by model distance: nonbonded pdb=" C3' G G 20 " pdb=" OP2 U G 21 " model vdw 1.865 2.776 nonbonded pdb=" ND2 ASN D 57 " pdb=" C5 U G 26 " model vdw 1.943 3.420 nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.967 2.520 nonbonded pdb=" OG1 THR B 126 " pdb=" OD1 ASN B 135 " model vdw 2.060 2.440 nonbonded pdb=" OG1 THR D 186 " pdb=" OP1 U G 30 " model vdw 2.160 2.440 ... (remaining 112350 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 individual isotropic 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: 4.580 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: 16.160 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 42.440 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 : 0.007 0.130 15188 Z= 0.439 Angle : 0.907 56.223 20595 Z= 0.485 Chirality : 0.052 0.427 2292 Planarity : 0.004 0.054 2536 Dihedral : 14.906 173.423 5876 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.98 % Favored : 92.96 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.48 % 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: 0.14 (0.28), residues: 343 loop : -1.99 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 339 HIS 0.018 0.002 HIS D 62 PHE 0.025 0.002 PHE C 166 TYR 0.021 0.002 TYR C 206 ARG 0.021 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 286 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 1.809 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 outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.3310 time to fit residues: 131.1155 Evaluate side-chains 118 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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: 0.7980 chunk 133 optimal weight: 0.3980 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.0000 chunk 71 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN C 69 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS H 129 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15188 Z= 0.182 Angle : 0.613 11.458 20595 Z= 0.324 Chirality : 0.043 0.198 2292 Planarity : 0.004 0.042 2536 Dihedral : 13.941 179.022 2413 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.81 % Allowed : 9.28 % Favored : 88.91 % 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: -0.19 (0.20), residues: 1718 helix: 1.20 (0.21), residues: 642 sheet: 0.53 (0.28), residues: 353 loop : -1.74 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 52 HIS 0.017 0.001 HIS A 72 PHE 0.020 0.001 PHE D 148 TYR 0.025 0.001 TYR H 255 ARG 0.008 0.001 ARG F 22 *********************** 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 167 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.813 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: E 82 LEU cc_start: 0.8125 (mm) cc_final: 0.7449 (tt) REVERT: H 13 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7296 (pttm) outliers start: 28 outliers final: 9 residues processed: 160 average time/residue: 0.3064 time to fit residues: 71.3642 Evaluate side-chains 110 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15188 Z= 0.411 Angle : 0.687 16.306 20595 Z= 0.363 Chirality : 0.045 0.428 2292 Planarity : 0.004 0.045 2536 Dihedral : 13.943 176.167 2413 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.00 % Allowed : 11.35 % Favored : 86.65 % 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: 1.26 (0.20), residues: 645 sheet: 0.48 (0.28), residues: 350 loop : -1.90 (0.20), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 339 HIS 0.008 0.002 HIS F 169 PHE 0.020 0.002 PHE H 163 TYR 0.030 0.002 TYR F 21 ARG 0.011 0.001 ARG F 405 *********************** 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 122 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7407 (tmm) cc_final: 0.7065 (tmm) REVERT: D 40 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8127 (tm-30) REVERT: F 163 MET cc_start: 0.7714 (mmm) cc_final: 0.7490 (mmt) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 0.2881 time to fit residues: 50.3511 Evaluate side-chains 101 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 207 ASP 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 F residue 13 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN H 17 HIS ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15188 Z= 0.212 Angle : 0.562 12.772 20595 Z= 0.296 Chirality : 0.042 0.292 2292 Planarity : 0.003 0.042 2536 Dihedral : 13.830 178.012 2413 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.58 % Allowed : 12.31 % Favored : 85.11 % 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: 0.06 (0.20), residues: 1718 helix: 1.60 (0.21), residues: 645 sheet: 0.66 (0.28), residues: 345 loop : -1.80 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 52 HIS 0.008 0.001 HIS A 72 PHE 0.020 0.001 PHE F 283 TYR 0.017 0.001 TYR F 21 ARG 0.008 0.001 ARG E 78 *********************** 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 138 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6188 (mt) REVERT: F 163 MET cc_start: 0.7778 (mmm) cc_final: 0.7568 (mmt) outliers start: 40 outliers final: 26 residues processed: 131 average time/residue: 0.2739 time to fit residues: 54.6480 Evaluate side-chains 112 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 207 ASP 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 129 GLN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 152 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15188 Z= 0.217 Angle : 0.565 13.632 20595 Z= 0.297 Chirality : 0.042 0.363 2292 Planarity : 0.003 0.052 2536 Dihedral : 13.748 177.732 2413 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 13.15 % Favored : 84.40 % 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: 0.19 (0.20), residues: 1718 helix: 1.74 (0.21), residues: 645 sheet: 0.77 (0.28), residues: 345 loop : -1.78 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 52 HIS 0.007 0.001 HIS A 72 PHE 0.022 0.001 PHE F 283 TYR 0.018 0.001 TYR F 21 ARG 0.006 0.000 ARG A 93 *********************** 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 125 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 87 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 MET cc_start: 0.7115 (mmp) cc_final: 0.6862 (mmp) outliers start: 38 outliers final: 25 residues processed: 119 average time/residue: 0.2751 time to fit residues: 50.1600 Evaluate side-chains 107 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 192 ILE 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 F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 164 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15188 Z= 0.174 Angle : 0.535 14.172 20595 Z= 0.279 Chirality : 0.041 0.217 2292 Planarity : 0.003 0.057 2536 Dihedral : 13.563 178.806 2413 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.58 % Allowed : 13.60 % Favored : 83.82 % 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: 0.42 (0.20), residues: 1718 helix: 2.02 (0.21), residues: 638 sheet: 0.89 (0.28), residues: 343 loop : -1.70 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 52 HIS 0.007 0.001 HIS A 72 PHE 0.020 0.001 PHE F 283 TYR 0.019 0.001 TYR D 206 ARG 0.005 0.000 ARG E 81 *********************** 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 133 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 55 MET cc_start: 0.7144 (mmp) cc_final: 0.6906 (mmp) REVERT: E 212 LYS cc_start: 0.5654 (tptt) cc_final: 0.4886 (ptpt) REVERT: F 1 MET cc_start: 0.6050 (ttt) cc_final: 0.5245 (ttt) REVERT: F 252 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7439 (p90) outliers start: 40 outliers final: 28 residues processed: 126 average time/residue: 0.2802 time to fit residues: 53.3100 Evaluate side-chains 114 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 207 ASP 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 F residue 13 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0030 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15188 Z= 0.146 Angle : 0.531 14.556 20595 Z= 0.275 Chirality : 0.040 0.161 2292 Planarity : 0.003 0.060 2536 Dihedral : 13.469 178.965 2413 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.26 % Allowed : 14.51 % Favored : 83.24 % 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: 0.54 (0.20), residues: 1718 helix: 2.11 (0.21), residues: 641 sheet: 1.01 (0.28), residues: 331 loop : -1.63 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 339 HIS 0.006 0.001 HIS E 174 PHE 0.019 0.001 PHE F 283 TYR 0.015 0.001 TYR E 154 ARG 0.007 0.000 ARG A 93 *********************** 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 125 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 90 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7143 (tmm) cc_final: 0.6761 (tmm) REVERT: E 55 MET cc_start: 0.7140 (mmp) cc_final: 0.6851 (mmp) REVERT: E 102 PHE cc_start: 0.6882 (m-80) cc_final: 0.6680 (m-80) REVERT: E 103 PHE cc_start: 0.6889 (m-80) cc_final: 0.6567 (m-80) REVERT: E 212 LYS cc_start: 0.5721 (tptt) cc_final: 0.4867 (ptpt) REVERT: F 1 MET cc_start: 0.6163 (ttt) cc_final: 0.5368 (ttt) REVERT: F 252 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7382 (p90) outliers start: 35 outliers final: 29 residues processed: 120 average time/residue: 0.2638 time to fit residues: 49.7773 Evaluate side-chains 114 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 149 ASP Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 207 ASP 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 304 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.0040 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 33 optimal weight: 0.0000 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.1980 chunk 154 optimal weight: 1.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15188 Z= 0.126 Angle : 0.524 15.360 20595 Z= 0.270 Chirality : 0.040 0.165 2292 Planarity : 0.003 0.062 2536 Dihedral : 13.413 179.325 2413 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.74 % Allowed : 15.02 % Favored : 83.24 % 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: 0.59 (0.20), residues: 1718 helix: 2.11 (0.21), residues: 643 sheet: 1.15 (0.28), residues: 331 loop : -1.63 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 339 HIS 0.003 0.000 HIS A 72 PHE 0.013 0.001 PHE F 283 TYR 0.020 0.001 TYR D 206 ARG 0.005 0.000 ARG A 93 *********************** 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 121 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6984 (tmm) cc_final: 0.6673 (tmm) REVERT: E 102 PHE cc_start: 0.6873 (m-80) cc_final: 0.6668 (m-80) REVERT: E 103 PHE cc_start: 0.6916 (m-80) cc_final: 0.6614 (m-80) REVERT: E 212 LYS cc_start: 0.5712 (tptt) cc_final: 0.4987 (ptpt) REVERT: F 1 MET cc_start: 0.6183 (ttt) cc_final: 0.5406 (ttt) REVERT: F 252 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7374 (p90) outliers start: 27 outliers final: 24 residues processed: 116 average time/residue: 0.2504 time to fit residues: 45.3052 Evaluate side-chains 111 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 207 ASP 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 F residue 13 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 158 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15188 Z= 0.186 Angle : 0.553 14.402 20595 Z= 0.286 Chirality : 0.041 0.200 2292 Planarity : 0.003 0.062 2536 Dihedral : 13.416 177.442 2413 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.87 % Allowed : 15.15 % Favored : 82.98 % 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: 0.60 (0.20), residues: 1718 helix: 2.13 (0.21), residues: 642 sheet: 1.15 (0.28), residues: 331 loop : -1.63 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 339 HIS 0.006 0.001 HIS E 174 PHE 0.016 0.001 PHE F 283 TYR 0.016 0.001 TYR E 154 ARG 0.005 0.000 ARG E 81 *********************** 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 117 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7115 (tmm) cc_final: 0.6839 (tmm) REVERT: E 103 PHE cc_start: 0.6916 (m-80) cc_final: 0.6641 (m-80) REVERT: E 212 LYS cc_start: 0.5743 (tptt) cc_final: 0.4982 (ptpt) REVERT: F 1 MET cc_start: 0.6353 (ttt) cc_final: 0.5490 (ttt) REVERT: F 49 ASP cc_start: 0.5535 (OUTLIER) cc_final: 0.4847 (t0) REVERT: F 252 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7458 (p90) outliers start: 29 outliers final: 27 residues processed: 112 average time/residue: 0.2656 time to fit residues: 46.1068 Evaluate side-chains 114 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 207 ASP 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 304 VAL Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 8.9990 chunk 102 optimal weight: 0.2980 chunk 79 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 110 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 HIS H 122 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15188 Z= 0.163 Angle : 0.551 15.811 20595 Z= 0.285 Chirality : 0.040 0.153 2292 Planarity : 0.003 0.063 2536 Dihedral : 13.428 178.006 2413 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.93 % Allowed : 15.15 % Favored : 82.91 % 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: 0.60 (0.20), residues: 1718 helix: 2.11 (0.21), residues: 642 sheet: 1.07 (0.28), residues: 338 loop : -1.59 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 339 HIS 0.003 0.001 HIS A 72 PHE 0.050 0.001 PHE H 121 TYR 0.027 0.001 TYR F 284 ARG 0.006 0.000 ARG E 81 ********************** 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 119 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7144 (tmm) cc_final: 0.6883 (tmm) REVERT: E 102 PHE cc_start: 0.6930 (m-80) cc_final: 0.6697 (m-80) REVERT: E 103 PHE cc_start: 0.6952 (m-80) cc_final: 0.6673 (m-80) REVERT: E 212 LYS cc_start: 0.5739 (tptt) cc_final: 0.4997 (ptpt) REVERT: F 1 MET cc_start: 0.6517 (ttt) cc_final: 0.5580 (ttt) REVERT: F 49 ASP cc_start: 0.5595 (OUTLIER) cc_final: 0.4912 (t0) REVERT: F 252 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7497 (p90) outliers start: 30 outliers final: 27 residues processed: 114 average time/residue: 0.2744 time to fit residues: 48.7847 Evaluate side-chains 115 residues out of total 1551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 122 ASN Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 165 HIS Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 357 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 0.0570 chunk 143 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 overall best weight: 0.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS H 122 ASN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.079540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056935 restraints weight = 69379.153| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 5.92 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 15188 Z= 0.223 Angle : 0.778 59.200 20595 Z= 0.453 Chirality : 0.042 0.561 2292 Planarity : 0.003 0.070 2536 Dihedral : 13.438 178.025 2413 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.00 % Allowed : 15.28 % Favored : 82.72 % Cbeta Deviations : 0.06 % 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: 0.60 (0.20), residues: 1718 helix: 2.11 (0.21), residues: 642 sheet: 1.07 (0.28), residues: 338 loop : -1.59 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 339 HIS 0.004 0.001 HIS A 72 PHE 0.043 0.001 PHE H 121 TYR 0.018 0.001 TYR F 284 ARG 0.037 0.000 ARG E 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.64 seconds wall clock time: 56 minutes 44.15 seconds (3404.15 seconds total)