Starting phenix.real_space_refine on Mon Dec 11 05:04:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/12_2023/8wpe_37714_updated.pdb" } resolution = 2.7 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= 0.000 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 P 71 5.49 5 Mg 1 5.21 5 S 76 5.16 5 C 10463 2.51 5 N 2807 2.21 5 O 3327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C GLU 196": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 16745 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8223 Classifications: {'peptide': 1006} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 968} Chain: "B" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3468 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 525 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "F" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 481 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 758 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'D3T': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.44, per 1000 atoms: 0.56 Number of scatterers: 16745 At special positions: 0 Unit cell: (130.31, 130.31, 136.95, 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) S 76 16.00 P 71 15.00 Mg 1 11.99 O 3327 8.00 N 2807 7.00 C 10463 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: 6.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3638 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 22 sheets defined 40.7% alpha, 17.1% beta 31 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 7.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 145 through 148 No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 449 through 473 removed outlier: 3.643A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.829A pdb=" N GLY A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 553 through 560 Processing helix chain 'A' and resid 577 through 590 Processing helix chain 'A' and resid 622 through 642 Processing helix chain 'A' and resid 647 through 671 removed outlier: 3.625A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 671 " --> pdb=" O VAL A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 702 Processing helix chain 'A' and resid 764 through 780 Processing helix chain 'A' and resid 837 through 856 Processing helix chain 'A' and resid 861 through 882 Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 906 through 917 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 968 through 983 Processing helix chain 'A' and resid 986 through 996 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.575A pdb=" N TYR B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 250 through 256 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.510A pdb=" N PHE B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 37 Proline residue: C 21 - end of helix removed outlier: 5.544A pdb=" N SER C 24 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN C 25 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN C 31 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER C 35 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 132 through 151 removed outlier: 4.282A pdb=" N ILE C 135 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP C 138 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS C 139 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 140 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 144 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 145 " --> pdb=" O LYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.832A pdb=" N GLN C 188 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE C 189 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 212 through 215 removed outlier: 3.671A pdb=" N GLY C 215 " --> pdb=" O TRP C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 215' Processing helix chain 'D' and resid 143 through 173 Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'E' and resid 141 through 163 Processing helix chain 'E' and resid 169 through 194 Processing helix chain 'F' and resid 143 through 172 removed outlier: 3.706A pdb=" N LYS F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 199 Processing helix chain 'G' and resid 141 through 163 Processing helix chain 'G' and resid 169 through 194 Processing sheet with id= A, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.577A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 136 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.511A pdb=" N VAL A 42 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.242A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 285 through 287 Processing sheet with id= E, first strand: chain 'A' and resid 428 through 431 removed outlier: 6.665A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N SER A 420 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 405 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 394 through 397 Processing sheet with id= G, first strand: chain 'A' and resid 822 through 826 removed outlier: 7.280A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.608A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.852A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 933 through 935 Processing sheet with id= K, first strand: chain 'A' and resid 299 through 305 removed outlier: 3.560A pdb=" N HIS A 319 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 799 through 802 removed outlier: 6.963A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.718A pdb=" N PHE B 69 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 174 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.020A pdb=" N LEU B 166 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B 208 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 95 through 97 removed outlier: 4.046A pdb=" N LEU B 132 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 214 through 219 removed outlier: 3.661A pdb=" N LYS B 214 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET B 218 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 264 " --> pdb=" O MET B 218 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 244 through 246 Processing sheet with id= R, first strand: chain 'B' and resid 301 through 304 Processing sheet with id= S, first strand: chain 'B' and resid 124 through 128 removed outlier: 7.373A pdb=" N ILE B 142 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU B 127 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 140 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 375 through 379 Processing sheet with id= U, first strand: chain 'C' and resid 3 through 5 Processing sheet with id= V, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.310A pdb=" N VAL C 62 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TRP C 119 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 64 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 154 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N CYS C 65 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR C 156 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR C 175 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N CYS C 157 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE C 177 " --> pdb=" O CYS C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= V 700 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 7.23 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2623 1.31 - 1.44: 4870 1.44 - 1.57: 9456 1.57 - 1.70: 140 1.70 - 1.83: 118 Bond restraints: 17207 Sorted by residual: bond pdb=" C4' D3T A2001 " pdb=" C3' D3T A2001 " ideal model delta sigma weight residual 1.287 1.518 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C4' DC H 35 " pdb=" C3' DC H 35 " ideal model delta sigma weight residual 1.523 1.325 0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" C4' D3T A2001 " pdb=" O4' D3T A2001 " ideal model delta sigma weight residual 1.614 1.426 0.188 2.00e-02 2.50e+03 8.80e+01 bond pdb=" C4' DC H 35 " pdb=" O4' DC H 35 " ideal model delta sigma weight residual 1.450 1.612 -0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C5 DC H 35 " pdb=" C6 DC H 35 " ideal model delta sigma weight residual 1.337 1.497 -0.160 2.00e-02 2.50e+03 6.36e+01 ... (remaining 17202 not shown) Histogram of bond angle deviations from ideal: 85.62 - 96.31: 3 96.31 - 106.99: 841 106.99 - 117.67: 12090 117.67 - 128.35: 10477 128.35 - 139.04: 136 Bond angle restraints: 23547 Sorted by residual: angle pdb=" C3' DG H 34 " pdb=" O3' DG H 34 " pdb=" P DC H 35 " ideal model delta sigma weight residual 120.20 95.47 24.73 1.50e+00 4.44e-01 2.72e+02 angle pdb=" O3' DG H 34 " pdb=" P DC H 35 " pdb=" OP2 DC H 35 " ideal model delta sigma weight residual 108.00 139.04 -31.04 3.00e+00 1.11e-01 1.07e+02 angle pdb=" CG1 ILE D 156 " pdb=" CB ILE D 156 " pdb=" CG2 ILE D 156 " ideal model delta sigma weight residual 110.70 85.62 25.08 3.00e+00 1.11e-01 6.99e+01 angle pdb=" O3' DG H 34 " pdb=" P DC H 35 " pdb=" OP1 DC H 35 " ideal model delta sigma weight residual 108.00 86.15 21.85 3.00e+00 1.11e-01 5.30e+01 angle pdb=" CA GLN B 48 " pdb=" CB GLN B 48 " pdb=" CG GLN B 48 " ideal model delta sigma weight residual 114.10 126.76 -12.66 2.00e+00 2.50e-01 4.01e+01 ... (remaining 23542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.19: 9697 31.19 - 62.37: 550 62.37 - 93.56: 13 93.56 - 124.74: 1 124.74 - 155.93: 1 Dihedral angle restraints: 10262 sinusoidal: 4640 harmonic: 5622 Sorted by residual: dihedral pdb=" CA GLU G 168 " pdb=" C GLU G 168 " pdb=" N ASP G 169 " pdb=" CA ASP G 169 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA GLU B 139 " pdb=" C GLU B 139 " pdb=" N ASP B 140 " pdb=" CA ASP B 140 " ideal model delta harmonic sigma weight residual -180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" C ALA C 9 " pdb=" N ALA C 9 " pdb=" CA ALA C 9 " pdb=" CB ALA C 9 " ideal model delta harmonic sigma weight residual -122.60 -133.97 11.37 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 10259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2558 0.117 - 0.235: 107 0.235 - 0.352: 6 0.352 - 0.469: 1 0.469 - 0.587: 1 Chirality restraints: 2673 Sorted by residual: chirality pdb=" P DC H 35 " pdb=" OP1 DC H 35 " pdb=" OP2 DC H 35 " pdb=" O5' DC H 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.61e+00 chirality pdb=" CB ILE E 186 " pdb=" CA ILE E 186 " pdb=" CG1 ILE E 186 " pdb=" CG2 ILE E 186 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE C 117 " pdb=" CA ILE C 117 " pdb=" CG1 ILE C 117 " pdb=" CG2 ILE C 117 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 2670 not shown) Planarity restraints: 2738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 43 " -0.042 2.00e-02 2.50e+03 3.40e-02 2.90e+01 pdb=" CG TRP B 43 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP B 43 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 43 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 43 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 43 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 43 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 43 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 43 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 43 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 146 " -0.346 9.50e-02 1.11e+02 1.55e-01 1.49e+01 pdb=" NE ARG A 146 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 146 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 146 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 146 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 336 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" CD GLN A 336 " -0.066 2.00e-02 2.50e+03 pdb=" OE1 GLN A 336 " 0.025 2.00e-02 2.50e+03 pdb=" NE2 GLN A 336 " 0.022 2.00e-02 2.50e+03 ... (remaining 2735 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 461 2.70 - 3.25: 15431 3.25 - 3.80: 29923 3.80 - 4.35: 38882 4.35 - 4.90: 60741 Nonbonded interactions: 145438 Sorted by model distance: nonbonded pdb=" O3A D3T A2001 " pdb="MG MG A2002 " model vdw 2.147 2.170 nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A2002 " model vdw 2.161 2.170 nonbonded pdb=" OD1 ASP A 549 " pdb="MG MG A2002 " model vdw 2.205 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A2002 " model vdw 2.226 2.170 nonbonded pdb=" O3B D3T A2001 " pdb="MG MG A2002 " model vdw 2.240 2.170 ... (remaining 145433 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 'D' and (resid 139 through 201 or (resid 202 through 203 and (name N or n \ ame CA or name C or name O or name CB )))) selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 0.970 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: 0.020 Extract box with map and model: 6.360 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 54.560 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 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 0.231 17207 Z= 0.395 Angle : 0.977 31.037 23547 Z= 0.507 Chirality : 0.055 0.587 2673 Planarity : 0.008 0.155 2738 Dihedral : 17.149 155.928 6624 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.11 % 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: -1.50 (0.17), residues: 1884 helix: -0.83 (0.16), residues: 812 sheet: -0.69 (0.28), residues: 338 loop : -1.11 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP B 43 HIS 0.022 0.002 HIS C 8 PHE 0.040 0.002 PHE A 992 TYR 0.053 0.002 TYR B 89 ARG 0.021 0.001 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.988 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 1.2644 time to fit residues: 320.1659 Evaluate side-chains 152 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2965 time to fit residues: 3.0413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 36 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 HIS A 896 HIS A 918 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 261 HIS ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17207 Z= 0.260 Angle : 0.582 9.342 23547 Z= 0.317 Chirality : 0.042 0.212 2673 Planarity : 0.005 0.065 2738 Dihedral : 17.811 157.461 2837 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 1.66 % Allowed : 8.09 % Favored : 90.24 % 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: -0.39 (0.19), residues: 1884 helix: 0.45 (0.17), residues: 826 sheet: -0.63 (0.27), residues: 347 loop : -0.74 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 43 HIS 0.007 0.002 HIS A 170 PHE 0.021 0.002 PHE A 267 TYR 0.022 0.002 TYR A 458 ARG 0.008 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.017 Fit side-chains outliers start: 29 outliers final: 10 residues processed: 196 average time/residue: 1.4354 time to fit residues: 313.6717 Evaluate side-chains 152 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 1.829 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.2061 time to fit residues: 3.6539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 HIS A 675 ASN A 918 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS B 321 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN C 55 GLN C 133 HIS ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17207 Z= 0.389 Angle : 0.653 9.634 23547 Z= 0.353 Chirality : 0.044 0.206 2673 Planarity : 0.005 0.068 2738 Dihedral : 18.465 177.725 2837 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 3.21 % Allowed : 11.19 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1884 helix: 0.60 (0.18), residues: 835 sheet: -0.66 (0.28), residues: 311 loop : -0.60 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 43 HIS 0.005 0.002 HIS B 252 PHE 0.022 0.002 PHE A 267 TYR 0.023 0.002 TYR A 637 ARG 0.010 0.001 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 173 time to evaluate : 2.063 Fit side-chains outliers start: 56 outliers final: 24 residues processed: 205 average time/residue: 1.3536 time to fit residues: 311.8155 Evaluate side-chains 170 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.2779 time to fit residues: 5.6623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN C 146 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17207 Z= 0.198 Angle : 0.543 9.353 23547 Z= 0.294 Chirality : 0.040 0.156 2673 Planarity : 0.004 0.064 2738 Dihedral : 18.098 169.851 2837 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.87 % Rotamer: Outliers : 3.39 % Allowed : 13.61 % Favored : 83.01 % 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: 0.13 (0.19), residues: 1884 helix: 1.06 (0.18), residues: 823 sheet: -0.74 (0.27), residues: 339 loop : -0.49 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.003 0.001 HIS A 896 PHE 0.012 0.001 PHE A 630 TYR 0.022 0.001 TYR A 458 ARG 0.009 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 165 time to evaluate : 1.905 Fit side-chains outliers start: 59 outliers final: 27 residues processed: 203 average time/residue: 1.2931 time to fit residues: 294.8254 Evaluate side-chains 166 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.2517 time to fit residues: 4.1106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 303 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN C 146 GLN C 165 ASN C 199 ASN E 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17207 Z= 0.322 Angle : 0.612 9.512 23547 Z= 0.329 Chirality : 0.042 0.171 2673 Planarity : 0.004 0.066 2738 Dihedral : 18.273 165.694 2837 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.55 % Rotamer: Outliers : 3.27 % Allowed : 15.56 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1884 helix: 0.98 (0.18), residues: 835 sheet: -0.72 (0.28), residues: 319 loop : -0.46 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 212 HIS 0.005 0.001 HIS C 8 PHE 0.017 0.002 PHE A 630 TYR 0.026 0.002 TYR A 458 ARG 0.010 0.001 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 161 time to evaluate : 1.772 Fit side-chains outliers start: 57 outliers final: 35 residues processed: 205 average time/residue: 1.2541 time to fit residues: 289.5987 Evaluate side-chains 177 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.712 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.2204 time to fit residues: 4.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN D 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17207 Z= 0.242 Angle : 0.571 9.272 23547 Z= 0.306 Chirality : 0.041 0.165 2673 Planarity : 0.004 0.064 2738 Dihedral : 18.159 166.591 2837 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.08 % Favored : 96.76 % Rotamer: Outliers : 3.39 % Allowed : 15.96 % Favored : 80.65 % 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: 0.24 (0.19), residues: 1884 helix: 1.14 (0.18), residues: 828 sheet: -0.72 (0.27), residues: 325 loop : -0.43 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS B 252 PHE 0.013 0.001 PHE A 992 TYR 0.023 0.002 TYR A 458 ARG 0.011 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 160 time to evaluate : 2.017 Fit side-chains outliers start: 59 outliers final: 35 residues processed: 202 average time/residue: 1.2476 time to fit residues: 285.5343 Evaluate side-chains 180 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 4 average time/residue: 0.2321 time to fit residues: 4.1811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 184 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17207 Z= 0.258 Angle : 0.584 9.152 23547 Z= 0.312 Chirality : 0.041 0.189 2673 Planarity : 0.004 0.093 2738 Dihedral : 18.159 167.322 2837 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.18 % Favored : 96.55 % Rotamer: Outliers : 3.33 % Allowed : 16.76 % Favored : 79.91 % 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: 0.28 (0.19), residues: 1884 helix: 1.13 (0.18), residues: 831 sheet: -0.66 (0.28), residues: 325 loop : -0.38 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 839 PHE 0.017 0.002 PHE A 967 TYR 0.032 0.002 TYR A 458 ARG 0.017 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 158 time to evaluate : 1.962 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 39 residues processed: 202 average time/residue: 1.2225 time to fit residues: 279.1202 Evaluate side-chains 183 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 35 residues processed: 4 average time/residue: 0.2167 time to fit residues: 4.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17207 Z= 0.228 Angle : 0.586 13.060 23547 Z= 0.309 Chirality : 0.041 0.247 2673 Planarity : 0.004 0.064 2738 Dihedral : 18.085 167.920 2837 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.13 % Favored : 96.60 % Rotamer: Outliers : 3.04 % Allowed : 17.34 % Favored : 79.62 % 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: 0.25 (0.19), residues: 1884 helix: 1.11 (0.18), residues: 836 sheet: -0.62 (0.28), residues: 325 loop : -0.44 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS C 8 PHE 0.014 0.001 PHE A 992 TYR 0.036 0.002 TYR A 458 ARG 0.013 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 154 time to evaluate : 1.862 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 198 average time/residue: 1.2226 time to fit residues: 274.3703 Evaluate side-chains 186 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 0.5514 time to fit residues: 4.7387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17207 Z= 0.272 Angle : 0.601 11.845 23547 Z= 0.318 Chirality : 0.042 0.194 2673 Planarity : 0.004 0.064 2738 Dihedral : 18.120 168.379 2837 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.29 % Favored : 96.44 % Rotamer: Outliers : 2.93 % Allowed : 17.57 % Favored : 79.51 % 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 (0.19), residues: 1884 helix: 1.06 (0.18), residues: 836 sheet: -0.72 (0.28), residues: 320 loop : -0.43 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS B 252 PHE 0.024 0.002 PHE B 212 TYR 0.039 0.002 TYR A 458 ARG 0.010 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 149 time to evaluate : 1.971 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 39 residues processed: 189 average time/residue: 1.2072 time to fit residues: 257.7236 Evaluate side-chains 185 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 35 residues processed: 5 average time/residue: 0.2577 time to fit residues: 4.4606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 136 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17207 Z= 0.349 Angle : 0.653 11.563 23547 Z= 0.345 Chirality : 0.044 0.192 2673 Planarity : 0.005 0.067 2738 Dihedral : 18.253 169.020 2837 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.29 % Favored : 96.44 % Rotamer: Outliers : 2.53 % Allowed : 18.31 % Favored : 79.16 % 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: 0.05 (0.19), residues: 1884 helix: 0.90 (0.18), residues: 838 sheet: -0.72 (0.29), residues: 305 loop : -0.50 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 137 HIS 0.005 0.001 HIS C 8 PHE 0.021 0.002 PHE B 212 TYR 0.042 0.002 TYR A 458 ARG 0.011 0.001 ARG E 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 2.083 Fit side-chains outliers start: 44 outliers final: 33 residues processed: 180 average time/residue: 1.2180 time to fit residues: 247.5776 Evaluate side-chains 172 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 3 average time/residue: 0.2672 time to fit residues: 3.6211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 139 optimal weight: 0.0020 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 136 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.209253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.175992 restraints weight = 16928.194| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 1.90 r_work: 0.3820 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17207 Z= 0.189 Angle : 0.566 12.394 23547 Z= 0.299 Chirality : 0.041 0.270 2673 Planarity : 0.004 0.064 2738 Dihedral : 17.997 170.240 2837 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.08 % Favored : 96.71 % Rotamer: Outliers : 2.64 % Allowed : 18.48 % Favored : 78.87 % 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: 0.28 (0.20), residues: 1884 helix: 1.16 (0.18), residues: 831 sheet: -0.71 (0.28), residues: 320 loop : -0.41 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 839 PHE 0.019 0.001 PHE B 212 TYR 0.041 0.001 TYR A 458 ARG 0.010 0.000 ARG E 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5556.74 seconds wall clock time: 100 minutes 26.79 seconds (6026.79 seconds total)