Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 17:04:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ply_13506/08_2023/7ply_13506_updated.pdb" } resolution = 3.2 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= 0.001 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: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6471 2.51 5 N 1720 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6110 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.43, per 1000 atoms: 0.54 Number of scatterers: 10149 At special positions: 0 Unit cell: (106.7, 132, 150.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1891 8.00 N 1720 7.00 C 6471 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: 4.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 48.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.695A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 193 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.567A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.741A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.106A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.830A pdb=" N ASN A 497 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 500 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.620A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.700A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.543A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.406A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.745A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.944A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.655A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.775A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.216A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.179A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing sheet with id= A, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.133A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 50 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.701A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= D, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= E, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.599A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.901A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= H, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= I, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= J, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.564A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= L, first strand: chain 'B' and resid 26 through 28 452 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2903 1.33 - 1.46: 2846 1.46 - 1.60: 4514 1.60 - 1.73: 0 1.73 - 1.86: 102 Bond restraints: 10365 Sorted by residual: bond pdb=" C4 9UE C 404 " pdb=" C5 9UE C 404 " ideal model delta sigma weight residual 0.880 1.493 -0.613 2.00e-02 2.50e+03 9.38e+02 bond pdb=" C11 9UE C 404 " pdb=" C12 9UE C 404 " ideal model delta sigma weight residual 2.064 1.523 0.541 2.00e-02 2.50e+03 7.32e+02 bond pdb=" C9 9UE C 404 " pdb=" N1 9UE C 404 " ideal model delta sigma weight residual 1.863 1.361 0.502 2.00e-02 2.50e+03 6.30e+02 bond pdb=" O 9UE C 404 " pdb=" C4 9UE C 404 " ideal model delta sigma weight residual 0.887 1.332 -0.445 2.00e-02 2.50e+03 4.94e+02 bond pdb=" C7 9UE C 404 " pdb=" C8 9UE C 404 " ideal model delta sigma weight residual 1.139 1.518 -0.379 2.00e-02 2.50e+03 3.60e+02 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.59: 227 105.59 - 113.55: 5739 113.55 - 121.51: 5876 121.51 - 129.48: 2088 129.48 - 137.44: 68 Bond angle restraints: 13998 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " ideal model delta sigma weight residual 73.46 132.01 -58.55 3.00e+00 1.11e-01 3.81e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C22 9UE C 404 " ideal model delta sigma weight residual 176.54 122.42 54.12 3.00e+00 1.11e-01 3.25e+02 angle pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 78.92 131.18 -52.26 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C13 9UE C 404 " pdb=" C14 9UE C 404 " pdb=" C16 9UE C 404 " ideal model delta sigma weight residual 67.70 114.08 -46.38 3.00e+00 1.11e-01 2.39e+02 angle pdb=" N3 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 73.72 117.27 -43.55 3.00e+00 1.11e-01 2.11e+02 ... (remaining 13993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 6072 32.13 - 64.26: 123 64.26 - 96.38: 29 96.38 - 128.51: 3 128.51 - 160.64: 3 Dihedral angle restraints: 6230 sinusoidal: 2556 harmonic: 3674 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 151.78 148.22 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" CA GLY A 563 " pdb=" C GLY A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA LYS C 61 " pdb=" C LYS C 61 " pdb=" N ARG C 62 " pdb=" CA ARG C 62 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1505 0.160 - 0.321: 18 0.321 - 0.481: 0 0.481 - 0.641: 1 0.641 - 0.801: 1 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C29 9UE C 404 " pdb=" C5 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -1.85 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C12 9UE C 404 " pdb=" C11 9UE C 404 " pdb=" C13 9UE C 404 " pdb=" C17 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.99 2.44 0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -2.40 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1522 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.134 9.50e-02 1.11e+02 7.44e-02 2.64e+01 pdb=" NE ARG C 147 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.084 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.108 9.50e-02 1.11e+02 6.22e-02 2.04e+01 pdb=" NE ARG A 278 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 88 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C HIS C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1758 2.76 - 3.30: 10013 3.30 - 3.83: 16305 3.83 - 4.37: 19307 4.37 - 4.90: 33644 Nonbonded interactions: 81027 Sorted by model distance: nonbonded pdb=" OD2 ASP A 507 " pdb=" OG SER C 350 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.288 2.520 nonbonded pdb=" NZ LYS A 246 " pdb=" OE1 GLN A 639 " model vdw 2.290 2.520 nonbonded pdb=" OE2 GLU A 511 " pdb=" N THR C 351 " model vdw 2.300 2.520 ... (remaining 81022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 1.390 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: 6.770 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.000 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.016 0.613 10365 Z= 1.078 Angle : 1.492 58.550 13998 Z= 0.680 Chirality : 0.066 0.801 1525 Planarity : 0.008 0.108 1792 Dihedral : 15.184 160.639 3862 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1237 helix: -0.99 (0.17), residues: 605 sheet: -0.26 (0.37), residues: 161 loop : -0.14 (0.26), residues: 471 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2763 time to fit residues: 54.4162 Evaluate side-chains 80 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 264 GLN A 354 HIS A 398 ASN A 406 HIS A 410 ASN A 455 ASN A 497 ASN A 638 HIS A 657 HIS C 137 GLN C 246 GLN B 75 GLN B 147 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10365 Z= 0.204 Angle : 0.847 47.194 13998 Z= 0.371 Chirality : 0.043 0.238 1525 Planarity : 0.004 0.054 1792 Dihedral : 9.811 174.179 1384 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1237 helix: 1.06 (0.20), residues: 611 sheet: 0.23 (0.39), residues: 158 loop : 0.64 (0.28), residues: 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 110 average time/residue: 0.1893 time to fit residues: 32.0042 Evaluate side-chains 81 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1053 time to fit residues: 1.8945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN C 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10365 Z= 0.290 Angle : 0.822 47.284 13998 Z= 0.355 Chirality : 0.043 0.207 1525 Planarity : 0.004 0.054 1792 Dihedral : 9.393 163.878 1384 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1237 helix: 1.50 (0.21), residues: 611 sheet: 0.57 (0.39), residues: 166 loop : 0.71 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 0.1873 time to fit residues: 27.3370 Evaluate side-chains 76 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1586 time to fit residues: 2.8627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 0.0970 chunk 58 optimal weight: 0.0980 chunk 12 optimal weight: 0.0470 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 726 GLN A 730 ASN C 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 0.030 10365 Z= 0.194 Angle : 0.779 47.331 13998 Z= 0.327 Chirality : 0.041 0.239 1525 Planarity : 0.004 0.052 1792 Dihedral : 8.724 147.573 1384 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 0.65 % 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: 1.70 (0.24), residues: 1237 helix: 1.69 (0.21), residues: 612 sheet: 0.57 (0.39), residues: 166 loop : 0.75 (0.30), residues: 459 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.2035 time to fit residues: 28.3960 Evaluate side-chains 82 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1753 time to fit residues: 2.6492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 0.0040 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 10365 Z= 0.315 Angle : 0.807 47.361 13998 Z= 0.345 Chirality : 0.042 0.250 1525 Planarity : 0.004 0.049 1792 Dihedral : 8.690 141.420 1384 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1237 helix: 1.70 (0.21), residues: 608 sheet: 0.62 (0.40), residues: 166 loop : 0.62 (0.29), residues: 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.1994 time to fit residues: 25.9649 Evaluate side-chains 80 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0980 time to fit residues: 2.8003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.205 Angle : 0.777 47.339 13998 Z= 0.323 Chirality : 0.041 0.259 1525 Planarity : 0.003 0.048 1792 Dihedral : 8.349 142.386 1384 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1237 helix: 1.76 (0.21), residues: 607 sheet: 0.64 (0.40), residues: 166 loop : 0.61 (0.29), residues: 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.2094 time to fit residues: 28.5183 Evaluate side-chains 79 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1236 time to fit residues: 2.3484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 10365 Z= 0.272 Angle : 0.805 47.342 13998 Z= 0.337 Chirality : 0.041 0.257 1525 Planarity : 0.004 0.047 1792 Dihedral : 8.347 143.572 1384 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1237 helix: 1.67 (0.21), residues: 613 sheet: 0.60 (0.40), residues: 166 loop : 0.56 (0.29), residues: 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 80 average time/residue: 0.2111 time to fit residues: 25.7329 Evaluate side-chains 75 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0973 time to fit residues: 1.8141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.003 0.032 10365 Z= 0.205 Angle : 0.788 47.327 13998 Z= 0.327 Chirality : 0.041 0.257 1525 Planarity : 0.003 0.046 1792 Dihedral : 8.201 144.072 1384 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.18 % 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: 1.61 (0.24), residues: 1237 helix: 1.68 (0.21), residues: 608 sheet: 0.56 (0.40), residues: 166 loop : 0.60 (0.29), residues: 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 0.2116 time to fit residues: 26.2893 Evaluate side-chains 73 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1143 time to fit residues: 2.0203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10365 Z= 0.224 Angle : 0.791 47.312 13998 Z= 0.329 Chirality : 0.041 0.262 1525 Planarity : 0.003 0.046 1792 Dihedral : 8.225 144.257 1384 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.18 % 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: 1.61 (0.24), residues: 1237 helix: 1.68 (0.21), residues: 609 sheet: 0.59 (0.41), residues: 166 loop : 0.60 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.2133 time to fit residues: 24.9460 Evaluate side-chains 73 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1066 time to fit residues: 1.9682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 78 optimal weight: 0.0170 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 10365 Z= 0.206 Angle : 0.787 47.312 13998 Z= 0.326 Chirality : 0.041 0.264 1525 Planarity : 0.003 0.046 1792 Dihedral : 8.184 144.471 1384 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1237 helix: 1.73 (0.21), residues: 609 sheet: 0.52 (0.40), residues: 167 loop : 0.61 (0.29), residues: 461 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2474 Ramachandran restraints generated. 1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2124 time to fit residues: 25.2606 Evaluate side-chains 71 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067938 restraints weight = 21196.925| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.18 r_work: 0.2868 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10365 Z= 0.178 Angle : 0.780 47.283 13998 Z= 0.322 Chirality : 0.040 0.265 1525 Planarity : 0.003 0.046 1792 Dihedral : 8.102 144.277 1384 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1237 helix: 1.78 (0.22), residues: 603 sheet: 0.50 (0.40), residues: 167 loop : 0.66 (0.29), residues: 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.81 seconds wall clock time: 38 minutes 30.14 seconds (2310.14 seconds total)