Starting phenix.real_space_refine (version: dev) on Mon Dec 12 09:02:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2022/6wwo_21942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2022/6wwo_21942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2022/6wwo_21942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2022/6wwo_21942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2022/6wwo_21942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2022/6wwo_21942_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 2": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "B ASP 26": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "K TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 504": "NH1" <-> "NH2" Residue "K PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 555": "NH1" <-> "NH2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 627": "OD1" <-> "OD2" Residue "K ARG 633": "NH1" <-> "NH2" Residue "K ARG 654": "NH1" <-> "NH2" Residue "K ARG 683": "NH1" <-> "NH2" Residue "K GLU 690": "OE1" <-> "OE2" Residue "K ARG 728": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9784 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "K" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2816 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 11, 'TRANS': 349} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.98, per 1000 atoms: 0.61 Number of scatterers: 9784 At special positions: 0 Unit cell: (110.124, 74.52, 113.436, 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 63 16.00 P 8 15.00 Mg 2 11.99 O 1914 8.00 N 1667 7.00 C 6130 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: 4.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 8 sheets defined 35.8% alpha, 44.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.916A pdb=" N THR A 41 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 79 removed outlier: 4.647A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.880A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.755A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 4.020A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 237 Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.823A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.693A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.423A pdb=" N VAL A 409 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY A 410 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.859A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 374 through 389 removed outlier: 4.331A pdb=" N GLN B 384 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.735A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 removed outlier: 4.539A pdb=" N GLU B 410 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 424 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR B 425 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 463 through 472 removed outlier: 3.797A pdb=" N PHE K 471 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU K 472 " --> pdb=" O ASP K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 513 Processing helix chain 'K' and resid 577 through 590 removed outlier: 4.206A pdb=" N SER K 582 " --> pdb=" O SER K 578 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP K 583 " --> pdb=" O ASP K 579 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS K 589 " --> pdb=" O GLU K 585 " (cutoff:3.500A) Processing helix chain 'K' and resid 654 through 676 removed outlier: 3.511A pdb=" N VAL K 659 " --> pdb=" O LEU K 655 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER K 660 " --> pdb=" O LYS K 656 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS K 670 " --> pdb=" O LEU K 666 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE K 672 " --> pdb=" O LEU K 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 688 through 690 No H-bonds generated for 'chain 'K' and resid 688 through 690' Processing helix chain 'K' and resid 693 through 696 No H-bonds generated for 'chain 'K' and resid 693 through 696' Processing helix chain 'K' and resid 698 through 701 No H-bonds generated for 'chain 'K' and resid 698 through 701' Processing helix chain 'K' and resid 717 through 719 No H-bonds generated for 'chain 'K' and resid 717 through 719' Processing helix chain 'K' and resid 723 through 735 removed outlier: 3.735A pdb=" N GLN K 732 " --> pdb=" O ARG K 728 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG K 734 " --> pdb=" O ALA K 730 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU K 735 " --> pdb=" O THR K 731 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 7.316A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 269 through 271 removed outlier: 6.848A pdb=" N LYS A 352 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TYR A 319 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A 354 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY A 321 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 63 through 66 removed outlier: 8.357A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLY B 132 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE B 7 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 134 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ALA B 9 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR B 136 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= E, first strand: chain 'K' and resid 0 through 393 No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'K' and resid 395 through 400 removed outlier: 6.590A pdb=" N CYS K 477 " --> pdb=" O ALA K 708 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE K 710 " --> pdb=" O CYS K 477 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE K 479 " --> pdb=" O ILE K 710 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N THR K 712 " --> pdb=" O PHE K 479 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR K 481 " --> pdb=" O THR K 712 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER K 528 " --> pdb=" O THR K 610 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 416 through 419 removed outlier: 4.178A pdb=" N GLU K 422 " --> pdb=" O ASN K 419 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 555 through 559 removed outlier: 4.061A pdb=" N ARG K 555 " --> pdb=" O GLU K 567 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 852 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: 2.63 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1779 1.32 - 1.44: 2601 1.44 - 1.57: 5505 1.57 - 1.69: 11 1.69 - 1.81: 102 Bond restraints: 9998 Sorted by residual: bond pdb=" C22 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sigma weight residual 1.335 1.457 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" O3A ANP K 802 " pdb=" PB ANP K 802 " ideal model delta sigma weight residual 1.700 1.581 0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C12 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 1.337 1.455 -0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" C27 TA1 B 502 " pdb=" O11 TA1 B 502 " ideal model delta sigma weight residual 1.329 1.444 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" N3B ANP K 802 " pdb=" PG ANP K 802 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 9993 not shown) Histogram of bond angle deviations from ideal: 79.39 - 91.22: 3 91.22 - 103.06: 118 103.06 - 114.89: 6015 114.89 - 126.72: 7312 126.72 - 138.56: 132 Bond angle restraints: 13580 Sorted by residual: angle pdb=" CA PRO B 272 " pdb=" N PRO B 272 " pdb=" CD PRO B 272 " ideal model delta sigma weight residual 112.00 90.76 21.24 1.40e+00 5.10e-01 2.30e+02 angle pdb=" C ALA B 271 " pdb=" N PRO B 272 " pdb=" CA PRO B 272 " ideal model delta sigma weight residual 119.84 132.86 -13.02 1.25e+00 6.40e-01 1.08e+02 angle pdb=" N PRO B 272 " pdb=" CA PRO B 272 " pdb=" CB PRO B 272 " ideal model delta sigma weight residual 103.25 112.70 -9.45 1.05e+00 9.07e-01 8.10e+01 angle pdb=" CA ASN K 662 " pdb=" C ASN K 662 " pdb=" O ASN K 662 " ideal model delta sigma weight residual 120.42 113.94 6.48 1.06e+00 8.90e-01 3.73e+01 angle pdb=" CA PRO B 272 " pdb=" C PRO B 272 " pdb=" O PRO B 272 " ideal model delta sigma weight residual 120.60 109.93 10.67 1.82e+00 3.02e-01 3.44e+01 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 5710 31.41 - 62.82: 204 62.82 - 94.23: 12 94.23 - 125.64: 2 125.64 - 157.05: 2 Dihedral angle restraints: 5930 sinusoidal: 2374 harmonic: 3556 Sorted by residual: dihedral pdb=" CD ARG K 644 " pdb=" NE ARG K 644 " pdb=" CZ ARG K 644 " pdb=" NH1 ARG K 644 " ideal model delta sinusoidal sigma weight residual 0.00 -61.95 61.95 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -52.46 157.05 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 114.38 146.49 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 5927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1385 0.103 - 0.206: 101 0.206 - 0.309: 6 0.309 - 0.412: 2 0.412 - 0.515: 2 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.65 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CA PRO B 272 " pdb=" N PRO B 272 " pdb=" C PRO B 272 " pdb=" CB PRO B 272 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA VAL K 621 " pdb=" N VAL K 621 " pdb=" C VAL K 621 " pdb=" CB VAL K 621 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1493 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 644 " 0.943 9.50e-02 1.11e+02 4.23e-01 1.08e+02 pdb=" NE ARG K 644 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG K 644 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG K 644 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG K 644 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 401 " 0.814 9.50e-02 1.11e+02 3.65e-01 8.10e+01 pdb=" NE ARG K 401 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG K 401 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG K 401 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG K 401 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 271 " 0.148 5.00e-02 4.00e+02 1.94e-01 6.02e+01 pdb=" N PRO B 272 " -0.332 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " 0.122 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " 0.062 5.00e-02 4.00e+02 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 83 2.55 - 3.14: 7638 3.14 - 3.72: 14721 3.72 - 4.31: 21681 4.31 - 4.90: 36706 Nonbonded interactions: 80829 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.958 2.170 nonbonded pdb=" OG SER K 489 " pdb="MG MG K 801 " model vdw 1.999 2.170 nonbonded pdb=" OE2 GLU A 71 " pdb="MG MG A 502 " model vdw 2.015 2.170 nonbonded pdb=" OG1 THR A 179 " pdb=" O3' GTP A 501 " model vdw 2.070 2.440 nonbonded pdb=" O06 TA1 B 502 " pdb=" O07 TA1 B 502 " model vdw 2.100 2.440 ... (remaining 80824 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6130 2.51 5 N 1667 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.770 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: 15.790 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.080 Process input model: 28.320 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 0.011 0.122 9998 Z= 0.707 Angle : 1.285 21.235 13580 Z= 0.748 Chirality : 0.062 0.515 1496 Planarity : 0.019 0.423 1755 Dihedral : 15.864 157.055 3648 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.13 % Favored : 93.55 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.26 % 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: -4.55 (0.19), residues: 1224 helix: -2.84 (0.18), residues: 470 sheet: -2.63 (0.31), residues: 218 loop : -3.27 (0.21), residues: 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 276 time to evaluate : 1.137 Fit side-chains outliers start: 21 outliers final: 2 residues processed: 288 average time/residue: 1.0433 time to fit residues: 325.3176 Evaluate side-chains 217 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.6049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 358 GLN B 6 HIS B 28 HIS B 43 GLN B 57 ASN B 347 ASN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 391 ASN K 475 ASN K 483 GLN K 496 ASN K 626 HIS K 743 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9998 Z= 0.275 Angle : 0.643 10.317 13580 Z= 0.321 Chirality : 0.046 0.223 1496 Planarity : 0.006 0.123 1755 Dihedral : 9.689 161.327 1370 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.84 % Favored : 96.00 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.83 (0.22), residues: 1224 helix: -1.16 (0.23), residues: 466 sheet: -1.86 (0.30), residues: 250 loop : -2.47 (0.24), residues: 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 252 average time/residue: 0.9751 time to fit residues: 267.8827 Evaluate side-chains 243 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 10 residues processed: 11 average time/residue: 0.1308 time to fit residues: 3.9300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS B 195 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 298 ASN B 348 ASN K 649 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.083 9998 Z= 0.628 Angle : 0.769 9.984 13580 Z= 0.386 Chirality : 0.053 0.248 1496 Planarity : 0.006 0.106 1755 Dihedral : 9.841 164.751 1370 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer Outliers : 5.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -2.40 (0.22), residues: 1224 helix: -0.97 (0.23), residues: 466 sheet: -1.30 (0.31), residues: 249 loop : -2.24 (0.25), residues: 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 249 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 30 residues processed: 281 average time/residue: 1.0435 time to fit residues: 317.4248 Evaluate side-chains 253 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 21 residues processed: 9 average time/residue: 0.4074 time to fit residues: 6.0309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 98 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 300 ASN B 204 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9998 Z= 0.292 Angle : 0.618 10.335 13580 Z= 0.305 Chirality : 0.046 0.228 1496 Planarity : 0.005 0.092 1755 Dihedral : 9.560 164.692 1370 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer Outliers : 5.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.83 (0.23), residues: 1224 helix: -0.48 (0.24), residues: 475 sheet: -0.94 (0.33), residues: 246 loop : -1.98 (0.25), residues: 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 1.193 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 34 residues processed: 260 average time/residue: 1.0179 time to fit residues: 287.4322 Evaluate side-chains 255 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 221 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 25 residues processed: 10 average time/residue: 0.3045 time to fit residues: 5.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN B 204 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN K 512 GLN K 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9998 Z= 0.307 Angle : 0.615 10.364 13580 Z= 0.304 Chirality : 0.045 0.212 1496 Planarity : 0.005 0.087 1755 Dihedral : 9.473 164.722 1370 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.16 % Rotamer Outliers : 5.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 (0.23), residues: 1224 helix: -0.21 (0.24), residues: 474 sheet: -0.81 (0.33), residues: 243 loop : -1.77 (0.26), residues: 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 43 residues processed: 261 average time/residue: 1.0855 time to fit residues: 306.3232 Evaluate side-chains 269 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 30 residues processed: 14 average time/residue: 0.1387 time to fit residues: 4.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 chunk 118 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 113 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN B 204 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN B 334 GLN K 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9998 Z= 0.217 Angle : 0.578 10.798 13580 Z= 0.284 Chirality : 0.044 0.201 1496 Planarity : 0.005 0.084 1755 Dihedral : 9.280 164.585 1370 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.24 % Rotamer Outliers : 4.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.13 (0.24), residues: 1224 helix: 0.09 (0.25), residues: 475 sheet: -0.56 (0.34), residues: 241 loop : -1.58 (0.26), residues: 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 229 time to evaluate : 1.133 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 36 residues processed: 261 average time/residue: 1.0371 time to fit residues: 294.7612 Evaluate side-chains 264 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 228 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 8 average time/residue: 0.1644 time to fit residues: 3.6594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.0000 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 0.0270 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 0.0570 chunk 71 optimal weight: 0.0030 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 334 GLN K 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9998 Z= 0.145 Angle : 0.549 10.569 13580 Z= 0.266 Chirality : 0.042 0.188 1496 Planarity : 0.004 0.073 1755 Dihedral : 9.015 163.868 1370 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.81 (0.24), residues: 1224 helix: 0.43 (0.25), residues: 474 sheet: -0.43 (0.34), residues: 241 loop : -1.47 (0.25), residues: 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 1.127 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 30 residues processed: 273 average time/residue: 1.0554 time to fit residues: 312.3678 Evaluate side-chains 249 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 5 average time/residue: 0.1439 time to fit residues: 2.7811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 0.0470 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 106 optimal weight: 0.0070 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN K 512 GLN K 549 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9998 Z= 0.145 Angle : 0.558 9.591 13580 Z= 0.267 Chirality : 0.042 0.174 1496 Planarity : 0.005 0.075 1755 Dihedral : 8.939 163.815 1370 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.49 (0.24), residues: 1224 helix: 0.76 (0.26), residues: 460 sheet: -0.23 (0.35), residues: 241 loop : -1.31 (0.25), residues: 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 28 residues processed: 257 average time/residue: 1.0514 time to fit residues: 292.6963 Evaluate side-chains 247 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 219 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 3 average time/residue: 0.1477 time to fit residues: 2.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.4980 chunk 102 optimal weight: 0.0570 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.0370 chunk 47 optimal weight: 0.1980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.0270 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN B 247 ASN K 512 GLN K 549 GLN ** K 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 9998 Z= 0.141 Angle : 0.558 10.539 13580 Z= 0.268 Chirality : 0.043 0.191 1496 Planarity : 0.004 0.059 1755 Dihedral : 8.798 163.870 1370 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.33 (0.24), residues: 1224 helix: 0.83 (0.26), residues: 459 sheet: -0.02 (0.35), residues: 243 loop : -1.23 (0.26), residues: 522 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 1.120 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 29 residues processed: 243 average time/residue: 1.1127 time to fit residues: 291.7629 Evaluate side-chains 240 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 3 average time/residue: 0.1172 time to fit residues: 2.1352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 195 ASN ** K 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9998 Z= 0.192 Angle : 0.590 11.225 13580 Z= 0.282 Chirality : 0.044 0.214 1496 Planarity : 0.004 0.057 1755 Dihedral : 8.832 164.913 1370 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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 (0.24), residues: 1224 helix: 0.79 (0.25), residues: 462 sheet: -0.04 (0.35), residues: 241 loop : -1.20 (0.26), residues: 521 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 1.155 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 28 residues processed: 235 average time/residue: 1.1107 time to fit residues: 283.2292 Evaluate side-chains 229 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 27 residues processed: 3 average time/residue: 0.1426 time to fit residues: 2.3315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 0.0040 overall best weight: 0.2728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 414 GLN ** K 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117056 restraints weight = 12936.046| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.85 r_work: 0.3455 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9998 Z= 0.160 Angle : 0.571 11.171 13580 Z= 0.272 Chirality : 0.043 0.198 1496 Planarity : 0.004 0.053 1755 Dihedral : 8.786 165.022 1370 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -0.18 (0.25), residues: 1224 helix: 0.88 (0.26), residues: 453 sheet: 0.05 (0.36), residues: 239 loop : -1.04 (0.26), residues: 532 =============================================================================== Job complete usr+sys time: 4878.73 seconds wall clock time: 86 minutes 57.75 seconds (5217.75 seconds total)