Starting phenix.real_space_refine on Sun Mar 17 04:58:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_37714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_37714.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_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_37714/03_2024/8wpe_37714_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_37714_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_37714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_37714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_37714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpe_37714/03_2024/8wpe_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-dev-5265/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: 9.56, per 1000 atoms: 0.57 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: 7.17 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: 7.53 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: 6.92 Time building geometry restraints manager: 7.75 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: 1.790 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: 6.330 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 52.840 Find NCS groups from input model: 0.480 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.840 ------------------------------------------------------------------------------- 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 : 1.616 Fit side-chains revert: symmetry clash REVERT: A 620 GLU cc_start: 0.6817 (tp30) cc_final: 0.6526 (tp30) outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 1.2109 time to fit residues: 306.0776 Evaluate side-chains 152 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP 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 643 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17207 Z= 0.261 Angle : 0.587 9.417 23547 Z= 0.319 Chirality : 0.042 0.225 2673 Planarity : 0.005 0.065 2738 Dihedral : 17.914 157.387 2839 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 1.66 % Allowed : 8.15 % Favored : 90.18 % 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: -0.40 (0.19), residues: 1884 helix: 0.44 (0.17), residues: 826 sheet: -0.63 (0.27), residues: 347 loop : -0.75 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 43 HIS 0.006 0.001 HIS A 36 PHE 0.021 0.002 PHE A 267 TYR 0.022 0.002 TYR A 637 ARG 0.009 0.001 ARG A 634 *********************** 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 212 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 1.582 Fit side-chains REVERT: A 88 MET cc_start: 0.8417 (mmt) cc_final: 0.7841 (mmm) REVERT: A 140 TYR cc_start: 0.7196 (m-80) cc_final: 0.6951 (m-80) REVERT: B 48 GLN cc_start: 0.7091 (mp10) cc_final: 0.6868 (mm-40) REVERT: C 80 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6328 (tt0) REVERT: C 135 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7540 (tp) outliers start: 29 outliers final: 9 residues processed: 196 average time/residue: 1.3689 time to fit residues: 298.3125 Evaluate side-chains 153 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 135 ILE 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: 10.0000 chunk 47 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 643 GLN 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 83 ASN C 133 HIS ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17207 Z= 0.314 Angle : 0.602 9.484 23547 Z= 0.326 Chirality : 0.043 0.175 2673 Planarity : 0.005 0.067 2738 Dihedral : 18.119 160.677 2837 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 2.93 % Allowed : 11.48 % 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: -0.14 (0.19), residues: 1884 helix: 0.73 (0.18), residues: 831 sheet: -0.69 (0.27), residues: 332 loop : -0.62 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 43 HIS 0.004 0.001 HIS A 36 PHE 0.018 0.002 PHE A 267 TYR 0.021 0.002 TYR A 637 ARG 0.009 0.001 ARG E 177 *********************** 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 216 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 165 time to evaluate : 1.867 Fit side-chains REVERT: A 2 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.5902 (m-30) REVERT: A 700 SER cc_start: 0.7732 (p) cc_final: 0.7453 (m) REVERT: B 63 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.5304 (pm20) REVERT: C 8 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.5955 (p90) REVERT: C 80 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: G 182 MET cc_start: 0.3598 (OUTLIER) cc_final: 0.2936 (ttm) outliers start: 51 outliers final: 23 residues processed: 194 average time/residue: 1.3066 time to fit residues: 284.5607 Evaluate side-chains 173 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 174 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17207 Z= 0.213 Angle : 0.542 9.375 23547 Z= 0.294 Chirality : 0.040 0.156 2673 Planarity : 0.004 0.064 2738 Dihedral : 18.031 166.011 2837 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 3.16 % Allowed : 12.63 % Favored : 84.21 % 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: 0.15 (0.19), residues: 1884 helix: 1.05 (0.18), residues: 829 sheet: -0.66 (0.27), residues: 333 loop : -0.52 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 43 HIS 0.004 0.001 HIS A 461 PHE 0.013 0.001 PHE A 630 TYR 0.023 0.001 TYR A 458 ARG 0.010 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 221 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 166 time to evaluate : 1.923 Fit side-chains REVERT: A 2 ASP cc_start: 0.6439 (OUTLIER) cc_final: 0.6012 (m-30) REVERT: B 63 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5246 (pm20) REVERT: C 8 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.6819 (p90) REVERT: C 193 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6189 (mmp80) REVERT: G 182 MET cc_start: 0.3692 (OUTLIER) cc_final: 0.3107 (ttm) outliers start: 55 outliers final: 24 residues processed: 199 average time/residue: 1.1901 time to fit residues: 267.5159 Evaluate side-chains 174 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 2.9990 chunk 104 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 165 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- 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 825 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17207 Z= 0.233 Angle : 0.554 9.363 23547 Z= 0.299 Chirality : 0.041 0.157 2673 Planarity : 0.004 0.065 2738 Dihedral : 18.099 172.025 2837 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.66 % Rotamer: Outliers : 3.27 % Allowed : 14.87 % Favored : 81.86 % 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: 0.32 (0.19), residues: 1884 helix: 1.18 (0.18), residues: 828 sheet: -0.51 (0.29), residues: 316 loop : -0.44 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 461 PHE 0.013 0.001 PHE A 630 TYR 0.027 0.002 TYR A 458 ARG 0.010 0.000 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 223 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 166 time to evaluate : 1.760 Fit side-chains REVERT: A 2 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6033 (m-30) REVERT: A 765 ASP cc_start: 0.5832 (OUTLIER) cc_final: 0.5251 (m-30) REVERT: B 63 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5193 (pm20) REVERT: B 139 GLU cc_start: 0.5373 (OUTLIER) cc_final: 0.5020 (tp30) REVERT: C 8 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.6824 (p90) REVERT: G 182 MET cc_start: 0.3582 (OUTLIER) cc_final: 0.3099 (ttm) outliers start: 57 outliers final: 30 residues processed: 202 average time/residue: 1.1759 time to fit residues: 267.2612 Evaluate side-chains 185 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 461 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17207 Z= 0.375 Angle : 0.643 9.409 23547 Z= 0.345 Chirality : 0.044 0.185 2673 Planarity : 0.005 0.067 2738 Dihedral : 18.323 165.700 2837 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.56 % Favored : 96.28 % Rotamer: Outliers : 3.44 % Allowed : 15.38 % 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: 0.11 (0.19), residues: 1884 helix: 0.96 (0.18), residues: 832 sheet: -0.67 (0.29), residues: 313 loop : -0.47 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 212 HIS 0.005 0.002 HIS B 252 PHE 0.019 0.002 PHE A 267 TYR 0.025 0.002 TYR A 458 ARG 0.011 0.001 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 228 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 168 time to evaluate : 1.775 Fit side-chains REVERT: A 1 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.3983 (tmt) REVERT: A 2 ASP cc_start: 0.6572 (OUTLIER) cc_final: 0.6147 (m-30) REVERT: A 194 SER cc_start: 0.7905 (p) cc_final: 0.7366 (m) REVERT: A 546 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7630 (mt) REVERT: A 711 MET cc_start: 0.6542 (tpp) cc_final: 0.6307 (mpp) REVERT: B 139 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.5215 (tp30) REVERT: C 8 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.6811 (p90) REVERT: C 80 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: C 193 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6248 (mmp80) REVERT: G 182 MET cc_start: 0.3733 (OUTLIER) cc_final: 0.3213 (ttm) outliers start: 60 outliers final: 33 residues processed: 205 average time/residue: 1.1700 time to fit residues: 270.5248 Evaluate side-chains 190 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 149 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 350 ASN B 408 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3649 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= 0.351 Angle : 0.631 9.260 23547 Z= 0.339 Chirality : 0.043 0.170 2673 Planarity : 0.005 0.066 2738 Dihedral : 18.315 167.466 2837 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.13 % Favored : 96.66 % Rotamer: Outliers : 3.96 % Allowed : 15.96 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1884 helix: 0.92 (0.18), residues: 831 sheet: -0.67 (0.29), residues: 305 loop : -0.51 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 470 HIS 0.004 0.001 HIS A 36 PHE 0.019 0.002 PHE A 967 TYR 0.031 0.002 TYR A 458 ARG 0.013 0.001 ARG E 177 *********************** 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 231 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 162 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: A 546 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 711 MET cc_start: 0.6548 (tpp) cc_final: 0.6316 (mpp) REVERT: A 859 MET cc_start: 0.2799 (ppp) cc_final: 0.2333 (pmm) REVERT: B 139 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5156 (tp30) REVERT: C 8 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6825 (p90) REVERT: C 80 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: C 193 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6097 (mmp80) outliers start: 69 outliers final: 39 residues processed: 208 average time/residue: 1.1217 time to fit residues: 263.7209 Evaluate side-chains 191 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** C 165 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.3502 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= 0.208 Angle : 0.568 11.425 23547 Z= 0.303 Chirality : 0.041 0.200 2673 Planarity : 0.004 0.063 2738 Dihedral : 18.076 168.858 2837 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.87 % Favored : 96.87 % Rotamer: Outliers : 2.87 % Allowed : 18.03 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1884 helix: 1.21 (0.18), residues: 818 sheet: -0.55 (0.29), residues: 307 loop : -0.40 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.003 0.001 HIS A 896 PHE 0.015 0.001 PHE A 967 TYR 0.033 0.001 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 211 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 161 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6116 (m-30) REVERT: A 765 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5626 (m-30) REVERT: A 859 MET cc_start: 0.2472 (ppp) cc_final: 0.2079 (pmm) REVERT: C 8 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6967 (p90) REVERT: G 182 MET cc_start: 0.3720 (tmm) cc_final: 0.3124 (ttm) outliers start: 50 outliers final: 31 residues processed: 196 average time/residue: 1.1841 time to fit residues: 262.7280 Evaluate side-chains 180 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain G residue 168 GLU 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: 3.9990 chunk 160 optimal weight: 0.1980 chunk 171 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 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: 0.6556 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17207 Z= 0.327 Angle : 0.629 11.549 23547 Z= 0.334 Chirality : 0.043 0.201 2673 Planarity : 0.004 0.065 2738 Dihedral : 18.210 169.047 2837 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.29 % Favored : 96.44 % Rotamer: Outliers : 2.70 % Allowed : 18.31 % Favored : 78.99 % 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: 0.17 (0.19), residues: 1884 helix: 1.04 (0.18), residues: 825 sheet: -0.67 (0.29), residues: 310 loop : -0.45 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 212 HIS 0.004 0.001 HIS A 170 PHE 0.024 0.002 PHE B 212 TYR 0.027 0.002 TYR B 199 ARG 0.010 0.001 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 198 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 151 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6187 (m-30) REVERT: A 711 MET cc_start: 0.6478 (tpp) cc_final: 0.5531 (mpp) REVERT: A 859 MET cc_start: 0.2549 (ppp) cc_final: 0.2112 (pmm) REVERT: C 8 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.6877 (p90) REVERT: G 182 MET cc_start: 0.3857 (tmm) cc_final: 0.3198 (ttm) outliers start: 47 outliers final: 32 residues processed: 184 average time/residue: 1.2755 time to fit residues: 264.0883 Evaluate side-chains 179 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 15 optimal weight: 0.0970 chunk 117 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.3625 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= 0.214 Angle : 0.574 10.506 23547 Z= 0.305 Chirality : 0.041 0.184 2673 Planarity : 0.004 0.063 2738 Dihedral : 18.027 169.841 2837 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.13 % Favored : 96.60 % Rotamer: Outliers : 2.53 % Allowed : 18.83 % Favored : 78.65 % 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: 0.31 (0.20), residues: 1884 helix: 1.15 (0.18), residues: 825 sheet: -0.54 (0.29), residues: 302 loop : -0.42 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 212 HIS 0.003 0.001 HIS A 896 PHE 0.021 0.001 PHE B 212 TYR 0.037 0.002 TYR A 458 ARG 0.010 0.000 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 195 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: A 859 MET cc_start: 0.2527 (ppp) cc_final: 0.2076 (pmm) REVERT: C 8 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7005 (p90) outliers start: 44 outliers final: 29 residues processed: 182 average time/residue: 1.1767 time to fit residues: 241.6656 Evaluate side-chains 174 residues out of total 1744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain G residue 168 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 ASN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.207837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.174309 restraints weight = 16891.287| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.90 r_work: 0.3801 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3633 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= 0.220 Angle : 0.574 12.260 23547 Z= 0.304 Chirality : 0.041 0.184 2673 Planarity : 0.004 0.065 2738 Dihedral : 18.014 170.099 2837 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.08 % Favored : 96.66 % Rotamer: Outliers : 2.24 % Allowed : 19.12 % Favored : 78.65 % 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: 0.34 (0.20), residues: 1884 helix: 1.16 (0.18), residues: 831 sheet: -0.54 (0.29), residues: 302 loop : -0.38 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 137 HIS 0.003 0.001 HIS A 839 PHE 0.022 0.001 PHE A 108 TYR 0.028 0.001 TYR B 199 ARG 0.011 0.000 ARG E 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5331.18 seconds wall clock time: 95 minutes 58.11 seconds (5758.11 seconds total)