Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 22:45:47 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2021/6wwo_21942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2021/6wwo_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_2021/6wwo_21942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2021/6wwo_21942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2021/6wwo_21942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwo_21942/12_2021/6wwo_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 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 None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/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: {'GTP': 1, ' MG': 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: 6.07, per 1000 atoms: 0.62 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 Amimo 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: 4.16 Conformation dependent library (CDL) restraints added in 1.4 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: 1.06 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: 2.83 Time building geometry restraints manager: 4.51 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=" C5 ANP K 802 " pdb=" N7 ANP K 802 " ideal model delta sigma weight residual 1.387 1.325 0.062 1.00e-02 1.00e+04 3.82e+01 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=" C4 ANP K 802 " pdb=" N9 ANP K 802 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.68e+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=" C4 ANP K 802 " pdb=" C5 ANP K 802 " ideal model delta sigma weight residual 1.386 1.445 -0.059 1.00e-02 1.00e+04 3.48e+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=" C5 ANP K 802 " pdb=" C4 ANP K 802 " pdb=" N3 ANP K 802 " ideal model delta sigma weight residual 126.80 118.37 8.43 7.41e-01 1.82e+00 1.29e+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=" C5 ANP K 802 " pdb=" N7 ANP K 802 " pdb=" C8 ANP K 802 " ideal model delta sigma weight residual 103.67 107.33 -3.66 4.26e-01 5.51e+00 7.39e+01 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 5716 31.41 - 62.82: 203 62.82 - 94.23: 13 94.23 - 125.64: 2 125.64 - 157.05: 2 Dihedral angle restraints: 5936 sinusoidal: 2380 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 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1385 0.103 - 0.206: 104 0.206 - 0.309: 5 0.309 - 0.412: 2 0.412 - 0.515: 2 Chirality restraints: 1498 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 1495 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 Write .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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.730 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 29.040 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: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 58.780 ------------------------------------------------------------------------------- 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= 0.706 Angle : 1.275 21.235 13580 Z= 0.772 Chirality : 0.062 0.515 1498 Planarity : 0.019 0.423 1755 Dihedral : 15.903 157.055 3654 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.97 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 : 1.116 Fit side-chains outliers start: 21 outliers final: 2 residues processed: 288 average time/residue: 1.0012 time to fit residues: 312.6076 Evaluate side-chains 216 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.6071 ------------------------------------------------------------------------------- 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: 0.5980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 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 8 HIS A 107 HIS A 256 GLN A 358 GLN B 6 HIS B 28 HIS B 43 GLN B 57 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9998 Z= 0.271 Angle : 0.655 11.291 13580 Z= 0.327 Chirality : 0.046 0.234 1498 Planarity : 0.006 0.123 1755 Dihedral : 9.890 160.199 1376 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.08 % Favored : 95.75 % Rotamer Outliers : 3.60 % 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: -2.96 (0.22), residues: 1224 helix: -1.30 (0.22), residues: 471 sheet: -1.86 (0.30), residues: 246 loop : -2.55 (0.24), residues: 507 *********************** 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 264 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 226 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 243 average time/residue: 0.9604 time to fit residues: 254.5578 Evaluate side-chains 237 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 10 residues processed: 9 average time/residue: 0.3108 time to fit residues: 5.0941 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.0370 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN B 247 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9998 Z= 0.271 Angle : 0.617 10.455 13580 Z= 0.304 Chirality : 0.045 0.220 1498 Planarity : 0.005 0.097 1755 Dihedral : 9.711 162.314 1376 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.24 % Rotamer Outliers : 4.27 % 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: -2.10 (0.23), residues: 1224 helix: -0.55 (0.24), residues: 459 sheet: -1.36 (0.31), residues: 248 loop : -2.11 (0.25), residues: 517 *********************** 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 273 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 1.081 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 28 residues processed: 250 average time/residue: 0.9596 time to fit residues: 261.3118 Evaluate side-chains 233 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 15 residues processed: 13 average time/residue: 0.1384 time to fit residues: 4.4778 ------------------------------------------------------------------------------- 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: 0.1980 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.0020 chunk 74 optimal weight: 0.0870 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 195 ASN B 204 ASN B 256 ASN B 279 GLN B 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9998 Z= 0.169 Angle : 0.562 10.972 13580 Z= 0.275 Chirality : 0.043 0.209 1498 Planarity : 0.004 0.086 1755 Dihedral : 9.492 162.095 1376 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Rotamer Outliers : 3.32 % 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 (0.24), residues: 1224 helix: -0.07 (0.25), residues: 463 sheet: -0.92 (0.33), residues: 244 loop : -1.83 (0.25), residues: 517 *********************** 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 248 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 1.157 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 235 average time/residue: 1.0353 time to fit residues: 264.2460 Evaluate side-chains 230 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.1524 time to fit residues: 3.1428 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 B 204 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 424 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9998 Z= 0.230 Angle : 0.569 10.906 13580 Z= 0.280 Chirality : 0.044 0.198 1498 Planarity : 0.005 0.085 1755 Dihedral : 9.431 162.815 1376 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer Outliers : 4.27 % 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: -1.26 (0.24), residues: 1224 helix: 0.07 (0.25), residues: 471 sheet: -0.70 (0.34), residues: 243 loop : -1.71 (0.26), residues: 510 *********************** 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 269 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 31 residues processed: 246 average time/residue: 1.0792 time to fit residues: 287.7082 Evaluate side-chains 241 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 17 residues processed: 14 average time/residue: 0.2562 time to fit residues: 6.5692 ------------------------------------------------------------------------------- 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: 0.0670 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 9 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 298 ASN K 512 GLN K 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9998 Z= 0.194 Angle : 0.560 11.190 13580 Z= 0.276 Chirality : 0.043 0.195 1498 Planarity : 0.004 0.079 1755 Dihedral : 9.354 162.833 1376 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % 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: -1.01 (0.24), residues: 1224 helix: 0.35 (0.25), residues: 465 sheet: -0.55 (0.34), residues: 243 loop : -1.64 (0.26), residues: 516 *********************** 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 257 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 239 average time/residue: 1.0289 time to fit residues: 267.4253 Evaluate side-chains 241 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.3062 time to fit residues: 3.8555 ------------------------------------------------------------------------------- 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: 2.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 72 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 GLN K 590 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9998 Z= 0.276 Angle : 0.596 11.199 13580 Z= 0.293 Chirality : 0.045 0.368 1498 Planarity : 0.005 0.075 1755 Dihedral : 9.400 163.836 1376 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.00 % Favored : 95.83 % 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: -0.97 (0.24), residues: 1224 helix: 0.28 (0.25), residues: 473 sheet: -0.56 (0.34), residues: 241 loop : -1.52 (0.26), residues: 510 *********************** 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 270 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 27 residues processed: 253 average time/residue: 1.0743 time to fit residues: 295.2085 Evaluate side-chains 248 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.124 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 18 residues processed: 10 average time/residue: 0.2551 time to fit residues: 4.9224 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 GLN K 590 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4065 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= 0.220 Angle : 0.578 10.958 13580 Z= 0.283 Chirality : 0.044 0.265 1498 Planarity : 0.005 0.075 1755 Dihedral : 9.362 163.748 1376 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer Outliers : 3.13 % 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: -0.90 (0.24), residues: 1224 helix: 0.30 (0.25), residues: 482 sheet: -0.48 (0.34), residues: 241 loop : -1.49 (0.26), residues: 501 *********************** 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 254 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 243 average time/residue: 1.0476 time to fit residues: 276.7572 Evaluate side-chains 238 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 7 average time/residue: 0.1255 time to fit residues: 3.1158 ------------------------------------------------------------------------------- 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: 6.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 71 optimal weight: 0.2980 chunk 115 optimal weight: 0.0970 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 GLN ** 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: 0.7686 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9998 Z= 0.163 Angle : 0.569 11.281 13580 Z= 0.276 Chirality : 0.043 0.299 1498 Planarity : 0.004 0.066 1755 Dihedral : 9.261 163.379 1376 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer Outliers : 2.65 % 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: -0.66 (0.24), residues: 1224 helix: 0.60 (0.25), residues: 474 sheet: -0.28 (0.35), residues: 236 loop : -1.46 (0.26), residues: 514 *********************** 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 253 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 225 time to evaluate : 1.174 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 244 average time/residue: 1.0389 time to fit residues: 275.7266 Evaluate side-chains 240 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.4412 time to fit residues: 3.6906 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 103 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 GLN K 549 GLN ** K 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9998 Z= 0.253 Angle : 0.604 10.914 13580 Z= 0.293 Chirality : 0.045 0.245 1498 Planarity : 0.005 0.080 1755 Dihedral : 9.360 164.377 1376 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer Outliers : 2.84 % 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: -0.70 (0.24), residues: 1224 helix: 0.53 (0.25), residues: 476 sheet: -0.31 (0.35), residues: 239 loop : -1.45 (0.26), residues: 509 ********************** 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 246 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 26 residues processed: 239 average time/residue: 1.0077 time to fit residues: 262.0878 Evaluate side-chains 236 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.1654 time to fit residues: 2.5760 ------------------------------------------------------------------------------- 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: 0.9980 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0020 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 GLN K 512 GLN K 549 GLN ** K 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115725 restraints weight = 12974.124| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.97 r_work: 0.3526 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work: 0.3500 rms_B_bonded: 1.82 restraints_weight: 0.1250 r_work: 0.3485 rms_B_bonded: 1.92 restraints_weight: 0.0625 r_work: 0.3469 rms_B_bonded: 2.06 restraints_weight: 0.0312 r_work: 0.3451 rms_B_bonded: 2.24 restraints_weight: 0.0156 r_work: 0.3431 rms_B_bonded: 2.47 restraints_weight: 0.0078 r_work: 0.3409 rms_B_bonded: 2.76 restraints_weight: 0.0039 r_work: 0.3384 rms_B_bonded: 3.11 restraints_weight: 0.0020 r_work: 0.3355 rms_B_bonded: 3.53 restraints_weight: 0.0010 r_work: 0.3323 rms_B_bonded: 4.02 restraints_weight: 0.0005 r_work: 0.3286 rms_B_bonded: 4.62 restraints_weight: 0.0002 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9998 Z= 0.219 Angle : 0.591 11.068 13580 Z= 0.289 Chirality : 0.045 0.254 1498 Planarity : 0.005 0.074 1755 Dihedral : 9.320 164.536 1376 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer Outliers : 2.75 % 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: -0.67 (0.24), residues: 1224 helix: 0.54 (0.25), residues: 477 sheet: -0.24 (0.35), residues: 234 loop : -1.45 (0.26), residues: 513 =============================================================================== Job complete usr+sys time: 4405.89 seconds wall clock time: 83 minutes 2.13 seconds (4982.13 seconds total)