Starting phenix.real_space_refine (version: 1.21rc1) on Thu May 4 17:55:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqx_20455/05_2023/6pqx_20455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqx_20455/05_2023/6pqx_20455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqx_20455/05_2023/6pqx_20455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqx_20455/05_2023/6pqx_20455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqx_20455/05_2023/6pqx_20455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pqx_20455/05_2023/6pqx_20455.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 120 5.49 5 S 36 5.16 5 C 6036 2.51 5 N 1758 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ASP 440": "OD1" <-> "OD2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E ARG 388": "NH1" <-> "NH2" Residue "E TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "E GLU 431": "OE1" <-> "OE2" Residue "E ARG 437": "NH1" <-> "NH2" Residue "E ASP 440": "OD1" <-> "OD2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 445": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E GLU 459": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 10116 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3826 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3826 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 462} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 284 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.42, per 1000 atoms: 0.54 Number of scatterers: 10116 At special positions: 0 Unit cell: (106.05, 89.25, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 36 16.00 P 120 15.00 O 2162 8.00 N 1758 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 57.3% alpha, 13.8% beta 50 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 39 through 53 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.504A pdb=" N CYS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.925A pdb=" N GLU A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 104 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.673A pdb=" N TYR A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 224 through 232 removed outlier: 4.664A pdb=" N TYR A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.754A pdb=" N SER A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 271 through 290 removed outlier: 3.830A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.879A pdb=" N ASP A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 4.281A pdb=" N PHE A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 4.179A pdb=" N THR A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.715A pdb=" N ILE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.617A pdb=" N ARG A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'E' and resid 25 through 37 Processing helix chain 'E' and resid 39 through 53 Processing helix chain 'E' and resid 61 through 73 removed outlier: 3.504A pdb=" N CYS E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 105 removed outlier: 3.925A pdb=" N GLU E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.673A pdb=" N TYR E 174 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 224 through 232 removed outlier: 4.663A pdb=" N TYR E 230 " --> pdb=" O LYS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.755A pdb=" N SER E 251 " --> pdb=" O PRO E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 271 through 290 removed outlier: 3.831A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 322 removed outlier: 3.879A pdb=" N ASP E 320 " --> pdb=" O ARG E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 4.280A pdb=" N PHE E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 removed outlier: 4.179A pdb=" N THR E 351 " --> pdb=" O PHE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.716A pdb=" N ILE E 362 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 398 Processing helix chain 'E' and resid 404 through 412 Processing helix chain 'E' and resid 413 through 421 Processing helix chain 'E' and resid 431 through 448 removed outlier: 3.618A pdb=" N ARG E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN E 438 " --> pdb=" O SER E 434 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 470 through 476 Processing helix chain 'E' and resid 489 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 164 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL A 178 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR A 149 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 180 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 147 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 119 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 156 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 117 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 116 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A 124 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP E 164 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 79 through 81 removed outlier: 6.277A pdb=" N VAL E 178 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 149 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE E 180 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE E 147 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE E 119 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU E 156 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE E 117 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU E 116 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N PHE E 124 " --> pdb=" O THR E 221 " (cutoff:3.500A) 414 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2498 1.33 - 1.45: 2517 1.45 - 1.57: 5247 1.57 - 1.69: 234 1.69 - 1.81: 56 Bond restraints: 10552 Sorted by residual: bond pdb=" O3' DA H 19 " pdb=" P DT H 20 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.20e+01 bond pdb=" O3' DC D 5 " pdb=" P DG D 6 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.19e+01 bond pdb=" O3' DA H 11 " pdb=" P DC H 12 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.11e+01 bond pdb=" O3' DA D 11 " pdb=" P DC D 12 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.50e-02 4.44e+03 7.56e+00 bond pdb=" O3' DA D 19 " pdb=" P DT D 20 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.88e+00 ... (remaining 10547 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.60: 713 105.60 - 112.72: 5672 112.72 - 119.83: 3628 119.83 - 126.94: 4391 126.94 - 134.05: 354 Bond angle restraints: 14758 Sorted by residual: angle pdb=" O3' DC H 5 " pdb=" C3' DC H 5 " pdb=" C2' DC H 5 " ideal model delta sigma weight residual 111.50 121.76 -10.26 1.50e+00 4.44e-01 4.68e+01 angle pdb=" C4' DG H 18 " pdb=" C3' DG H 18 " pdb=" O3' DG H 18 " ideal model delta sigma weight residual 110.00 103.09 6.91 1.50e+00 4.44e-01 2.12e+01 angle pdb=" O3' DG D 29 " pdb=" C3' DG D 29 " pdb=" C2' DG D 29 " ideal model delta sigma weight residual 111.50 104.61 6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" C4' DG D 18 " pdb=" C3' DG D 18 " pdb=" O3' DG D 18 " ideal model delta sigma weight residual 110.00 103.16 6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" O3' DG H 29 " pdb=" C3' DG H 29 " pdb=" C2' DG H 29 " ideal model delta sigma weight residual 111.50 104.71 6.79 1.50e+00 4.44e-01 2.05e+01 ... (remaining 14753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4724 17.40 - 34.79: 613 34.79 - 52.19: 377 52.19 - 69.58: 230 69.58 - 86.98: 26 Dihedral angle restraints: 5970 sinusoidal: 3142 harmonic: 2828 Sorted by residual: dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N PRO A 60 " pdb=" CA PRO A 60 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA TYR E 59 " pdb=" C TYR E 59 " pdb=" N PRO E 60 " pdb=" CA PRO E 60 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN E 135 " pdb=" C GLN E 135 " pdb=" N ASN E 136 " pdb=" CA ASN E 136 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1333 0.068 - 0.136: 301 0.136 - 0.204: 33 0.204 - 0.273: 4 0.273 - 0.341: 3 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C4' DA H 28 " pdb=" C5' DA H 28 " pdb=" O4' DA H 28 " pdb=" C3' DA H 28 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C4' DA D 28 " pdb=" C5' DA D 28 " pdb=" O4' DA D 28 " pdb=" C3' DA D 28 " both_signs ideal model delta sigma weight residual False -2.53 -2.19 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C3' DC H 5 " pdb=" C4' DC H 5 " pdb=" O3' DC H 5 " pdb=" C2' DC H 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.36 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1671 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC D 12 " 0.028 2.00e-02 2.50e+03 3.80e-02 3.25e+01 pdb=" N1 DC D 12 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DC D 12 " -0.041 2.00e-02 2.50e+03 pdb=" O2 DC D 12 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DC D 12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC D 12 " -0.069 2.00e-02 2.50e+03 pdb=" N4 DC D 12 " 0.072 2.00e-02 2.50e+03 pdb=" C5 DC D 12 " -0.014 2.00e-02 2.50e+03 pdb=" C6 DC D 12 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA C 29 " 0.017 2.00e-02 2.50e+03 3.07e-02 2.60e+01 pdb=" N9 DA C 29 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DA C 29 " 0.029 2.00e-02 2.50e+03 pdb=" N7 DA C 29 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA C 29 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA C 29 " 0.016 2.00e-02 2.50e+03 pdb=" N6 DA C 29 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DA C 29 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DA C 29 " 0.055 2.00e-02 2.50e+03 pdb=" N3 DA C 29 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DA C 29 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 29 " 0.008 2.00e-02 2.50e+03 3.05e-02 2.56e+01 pdb=" N9 DA G 29 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA G 29 " 0.030 2.00e-02 2.50e+03 pdb=" N7 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA G 29 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DA G 29 " 0.053 2.00e-02 2.50e+03 pdb=" N6 DA G 29 " -0.045 2.00e-02 2.50e+03 pdb=" N1 DA G 29 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA G 29 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DA G 29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA G 29 " -0.059 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1872 2.77 - 3.30: 10898 3.30 - 3.83: 19166 3.83 - 4.37: 21913 4.37 - 4.90: 32435 Nonbonded interactions: 86284 Sorted by model distance: nonbonded pdb=" NE ARG A 342 " pdb=" OP1 DA C 18 " model vdw 2.235 2.520 nonbonded pdb=" NH1 ARG E 485 " pdb=" OP1 DC G 17 " model vdw 2.243 2.520 nonbonded pdb=" O GLY A 126 " pdb="CA CA A 601 " model vdw 2.259 2.510 nonbonded pdb=" O ASP A 188 " pdb=" ND2 ASN A 192 " model vdw 2.260 2.520 nonbonded pdb=" O ASP E 188 " pdb=" ND2 ASN E 192 " model vdw 2.261 2.520 ... (remaining 86279 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.510 Find NCS groups from input model: 0.500 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.052 10552 Z= 0.352 Angle : 0.988 10.262 14758 Z= 0.601 Chirality : 0.058 0.341 1674 Planarity : 0.008 0.093 1450 Dihedral : 23.230 86.978 4134 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.23 % Favored : 94.14 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.21), residues: 956 helix: -2.19 (0.17), residues: 482 sheet: -1.76 (0.57), residues: 64 loop : -2.29 (0.26), residues: 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 99 average time/residue: 0.2056 time to fit residues: 24.3775 Evaluate side-chains 49 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.500 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0433 time to fit residues: 0.8457 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0158 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0056 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0270 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 54 optimal weight: 0.1980 chunk 42 optimal weight: 0.0040 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN E 179 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10552 Z= 0.204 Angle : 0.716 9.000 14758 Z= 0.389 Chirality : 0.039 0.137 1674 Planarity : 0.004 0.061 1450 Dihedral : 27.634 85.828 2222 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 2.51 % Favored : 97.07 % Rotamer Outliers : 0.47 % 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: -1.96 (0.24), residues: 956 helix: -0.65 (0.21), residues: 498 sheet: -0.96 (0.68), residues: 48 loop : -2.12 (0.27), residues: 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.1916 time to fit residues: 19.0619 Evaluate side-chains 50 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0717 time to fit residues: 0.7675 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0133 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0048 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0152 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0055 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0260 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 0.0020 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10552 Z= 0.204 Angle : 0.659 8.310 14758 Z= 0.364 Chirality : 0.038 0.163 1674 Planarity : 0.005 0.091 1450 Dihedral : 27.412 86.600 2222 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.02 % Favored : 94.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.26), residues: 956 helix: -0.42 (0.22), residues: 516 sheet: -1.03 (0.62), residues: 64 loop : -2.03 (0.29), residues: 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.436 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1547 time to fit residues: 13.1095 Evaluate side-chains 47 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6891 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0138 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0048 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0158 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0053 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0271 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 0.0070 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10552 Z= 0.203 Angle : 0.634 7.357 14758 Z= 0.354 Chirality : 0.038 0.138 1674 Planarity : 0.004 0.038 1450 Dihedral : 27.354 88.489 2222 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.86 % Favored : 93.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.26), residues: 956 helix: -0.48 (0.22), residues: 514 sheet: -0.49 (0.66), residues: 62 loop : -2.01 (0.29), residues: 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.430 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1568 time to fit residues: 14.1671 Evaluate side-chains 51 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.514 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6890 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0137 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0047 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0120 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0045 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0260 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0060 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 1.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10552 Z= 0.185 Angle : 0.618 7.286 14758 Z= 0.343 Chirality : 0.037 0.154 1674 Planarity : 0.004 0.035 1450 Dihedral : 27.206 78.888 2222 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.53 % Favored : 92.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.25), residues: 956 helix: -0.52 (0.22), residues: 512 sheet: -0.92 (0.65), residues: 64 loop : -2.04 (0.27), residues: 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.486 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1728 time to fit residues: 15.9114 Evaluate side-chains 53 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6430 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0128 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0044 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0150 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0053 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0239 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 10552 Z= 0.257 Angle : 0.666 7.585 14758 Z= 0.372 Chirality : 0.038 0.182 1674 Planarity : 0.005 0.076 1450 Dihedral : 27.240 85.266 2222 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.74 % Favored : 91.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 956 helix: -0.56 (0.22), residues: 508 sheet: -0.91 (0.61), residues: 70 loop : -1.93 (0.29), residues: 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.485 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1558 time to fit residues: 12.5024 Evaluate side-chains 46 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.464 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6158 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0117 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0049 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0141 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0051 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0244 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.0970 chunk 58 optimal weight: 0.0980 chunk 74 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 0.0370 overall best weight: 0.6636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10552 Z= 0.173 Angle : 0.622 7.535 14758 Z= 0.339 Chirality : 0.038 0.161 1674 Planarity : 0.004 0.070 1450 Dihedral : 27.256 85.432 2222 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.28 % Favored : 93.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 956 helix: -0.40 (0.23), residues: 512 sheet: -0.85 (0.59), residues: 70 loop : -2.12 (0.28), residues: 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.510 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1686 time to fit residues: 15.8576 Evaluate side-chains 54 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6665 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0136 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0150 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0056 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0261 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 0.0670 chunk 92 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10552 Z= 0.192 Angle : 0.625 8.243 14758 Z= 0.341 Chirality : 0.037 0.148 1674 Planarity : 0.004 0.058 1450 Dihedral : 27.146 85.072 2222 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.25), residues: 956 helix: -0.40 (0.22), residues: 526 sheet: -1.02 (0.67), residues: 64 loop : -2.15 (0.28), residues: 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1503 time to fit residues: 13.0937 Evaluate side-chains 48 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6283 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0120 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.009 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0046 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0231 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0083 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0264 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 0.0270 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10552 Z= 0.173 Angle : 0.624 8.479 14758 Z= 0.336 Chirality : 0.036 0.130 1674 Planarity : 0.004 0.041 1450 Dihedral : 27.084 86.687 2222 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 956 helix: -0.49 (0.22), residues: 536 sheet: -0.66 (0.64), residues: 70 loop : -2.15 (0.30), residues: 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.474 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1434 time to fit residues: 13.7786 Evaluate side-chains 52 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6553 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0129 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0049 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.013 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0158 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0060 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0227 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 105 optimal weight: 0.0050 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.0030 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10552 Z= 0.179 Angle : 0.634 13.046 14758 Z= 0.337 Chirality : 0.037 0.183 1674 Planarity : 0.004 0.044 1450 Dihedral : 26.957 83.118 2222 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.26), residues: 956 helix: -0.53 (0.22), residues: 520 sheet: -0.68 (0.64), residues: 70 loop : -2.05 (0.29), residues: 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 956 Ramachandran restraints generated. 478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1494 time to fit residues: 14.5156 Evaluate side-chains 55 residues out of total 427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6403 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0125 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.010 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0050 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0144 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.011 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0052 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0279 Evaluate side-chains 0 residues out of total 0 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4394 > 50: distance: 0 - 1: 35.594 distance: 1 - 2: 10.428 distance: 2 - 3: 28.014 distance: 2 - 4: 40.605 distance: 4 - 5: 53.999 distance: 5 - 6: 36.542 distance: 5 - 8: 58.717 distance: 6 - 7: 53.053 distance: 6 - 13: 46.007 distance: 8 - 9: 59.637 distance: 9 - 10: 58.431 distance: 10 - 11: 39.283 distance: 10 - 12: 15.996 distance: 13 - 14: 42.462 distance: 14 - 15: 41.043 distance: 15 - 17: 55.979 distance: 17 - 18: 68.839 distance: 18 - 19: 56.608 distance: 18 - 21: 57.054 distance: 19 - 20: 55.381 distance: 19 - 25: 12.172 distance: 21 - 22: 68.590 distance: 22 - 23: 68.082 distance: 22 - 24: 25.096 distance: 25 - 26: 58.517 distance: 26 - 27: 38.782 distance: 26 - 29: 55.035 distance: 27 - 28: 57.164 distance: 27 - 31: 46.285 distance: 29 - 30: 70.439 distance: 31 - 32: 57.620 distance: 32 - 33: 44.265 distance: 32 - 35: 51.435 distance: 33 - 34: 43.173 distance: 33 - 37: 38.496 distance: 35 - 36: 49.966 distance: 37 - 38: 36.409 distance: 38 - 39: 41.154 distance: 38 - 41: 57.321 distance: 39 - 40: 42.613 distance: 39 - 45: 54.888 distance: 41 - 42: 42.698 distance: 41 - 43: 45.696 distance: 42 - 44: 18.360 distance: 45 - 46: 58.865 distance: 46 - 47: 46.354 distance: 46 - 49: 46.250 distance: 47 - 48: 25.704 distance: 47 - 56: 49.168 distance: 49 - 50: 47.495 distance: 50 - 51: 53.767 distance: 50 - 52: 52.309 distance: 51 - 53: 56.006 distance: 52 - 54: 37.588 distance: 53 - 55: 45.387 distance: 54 - 55: 35.982 distance: 56 - 57: 46.399 distance: 57 - 58: 36.588 distance: 57 - 60: 44.874 distance: 58 - 59: 54.620 distance: 58 - 64: 32.908 distance: 60 - 61: 13.252 distance: 61 - 62: 11.250 distance: 62 - 63: 40.330 distance: 64 - 65: 39.377 distance: 65 - 68: 24.026 distance: 66 - 67: 34.354 distance: 68 - 69: 31.300 distance: 68 - 70: 47.195