Starting phenix.real_space_refine on Tue Sep 24 12:34:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/09_2024/7f4u_31454.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/09_2024/7f4u_31454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/09_2024/7f4u_31454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/09_2024/7f4u_31454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/09_2024/7f4u_31454.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4u_31454/09_2024/7f4u_31454.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5059 2.51 5 N 1476 2.21 5 O 1510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8079 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3416 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3298 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'PTRANS': 12, 'TRANS': 501} Chain breaks: 6 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 760 Unresolved non-hydrogen angles: 992 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'ASN:plan1': 5, 'TYR:plan': 4, 'UNK:plan-1': 50, 'TRP:plan': 4, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 403 Chain: "B" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 880 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 528 Unresolved non-hydrogen dihedrals: 176 Planarities with less than four sites: {'UNK:plan-1': 176} Unresolved non-hydrogen planarities: 176 Chain: "C" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Chain breaks: 5 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Time building chain proxies: 5.41, per 1000 atoms: 0.67 Number of scatterers: 8079 At special positions: 0 Unit cell: (78.11, 121.98, 189.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1510 8.00 N 1476 7.00 C 5059 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 - 3.00 Amino acid : True - 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: 2.28 Conformation dependent library (CDL) restraints added in 884.5 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 105.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.957A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.564A pdb=" N PHE A 91 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 removed outlier: 4.442A pdb=" N PHE A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.602A pdb=" N GLU A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 4.423A pdb=" N GLN A 140 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 167 removed outlier: 6.424A pdb=" N VAL A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.968A pdb=" N LEU A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.074A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.560A pdb=" N LYS A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Proline residue: A 236 - end of helix removed outlier: 4.323A pdb=" N GLN A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.506A pdb=" N GLN A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.966A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 331 through 349 Processing helix chain 'A' and resid 353 through 370 removed outlier: 4.440A pdb=" N GLN A 370 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.072A pdb=" N CYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 416 removed outlier: 4.053A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.544A pdb=" N LYS A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'B' and resid 167 through 185 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 198 through 208 removed outlier: 3.813A pdb=" N UNK B 202 " --> pdb=" O UNK B 198 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N UNK B 208 " --> pdb=" O UNK B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.536A pdb=" N UNK B 216 " --> pdb=" O UNK B 213 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK B 217 " --> pdb=" O UNK B 214 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N UNK B 222 " --> pdb=" O UNK B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 261 removed outlier: 4.687A pdb=" N ASP B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLU B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 removed outlier: 3.998A pdb=" N ALA B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 301 Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 325 removed outlier: 3.525A pdb=" N LEU B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 341 removed outlier: 3.819A pdb=" N ALA B 335 " --> pdb=" O PRO B 331 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.602A pdb=" N ASP B 372 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.797A pdb=" N ASN B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 411 removed outlier: 3.674A pdb=" N THR B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 411 " --> pdb=" O TYR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.864A pdb=" N GLN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 495 removed outlier: 3.987A pdb=" N LEU B 487 " --> pdb=" O ARG B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 515 removed outlier: 3.537A pdb=" N LEU B 511 " --> pdb=" O HIS B 507 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 removed outlier: 3.697A pdb=" N ALA B 522 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 568 Processing helix chain 'B' and resid 617 through 641 Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.760A pdb=" N CYS B 646 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 647 " --> pdb=" O ASP B 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 643 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 3.657A pdb=" N ALA B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 665 through 683 Processing helix chain 'B' and resid 687 through 693 removed outlier: 3.642A pdb=" N ILE B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 692 " --> pdb=" O GLN B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 708 Processing helix chain 'B' and resid 715 through 723 removed outlier: 4.281A pdb=" N LEU B 719 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 730 through 748 removed outlier: 5.027A pdb=" N ASP B 736 " --> pdb=" O PRO B 732 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 745 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 771 removed outlier: 3.736A pdb=" N VAL B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 873 Processing helix chain 'B' and resid 878 through 892 removed outlier: 4.064A pdb=" N UNK B 882 " --> pdb=" O UNK B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 915 Processing helix chain 'B' and resid 924 through 935 Processing helix chain 'B' and resid 939 through 954 Processing helix chain 'B' and resid 978 through 991 removed outlier: 4.492A pdb=" N UNK B 990 " --> pdb=" O UNK B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1003 removed outlier: 3.800A pdb=" N UNK B 999 " --> pdb=" O UNK B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1028 Processing helix chain 'B' and resid 1046 through 1051 removed outlier: 3.510A pdb=" N UNK B1051 " --> pdb=" O UNK B1047 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1067 Processing helix chain 'B' and resid 1068 through 1070 No H-bonds generated for 'chain 'B' and resid 1068 through 1070' Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.769A pdb=" N UNK C 47 " --> pdb=" O UNK C 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK C 48 " --> pdb=" O UNK C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 removed outlier: 4.543A pdb=" N UNK C 76 " --> pdb=" O UNK C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 144 through 163 Processing helix chain 'C' and resid 177 through 188 removed outlier: 4.750A pdb=" N UNK C 186 " --> pdb=" O UNK C 182 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1764 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: 2.21 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2841 1.34 - 1.46: 1508 1.46 - 1.58: 3756 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 8159 Sorted by residual: bond pdb=" N ASP B 540 " pdb=" CA ASP B 540 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.21e-02 6.83e+03 5.07e+00 bond pdb=" N GLU B 539 " pdb=" CA GLU B 539 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.65e+00 bond pdb=" CA ASP B 540 " pdb=" CB ASP B 540 " ideal model delta sigma weight residual 1.533 1.509 0.024 1.72e-02 3.38e+03 1.95e+00 bond pdb=" CA VAL B 306 " pdb=" CB VAL B 306 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.36e-02 5.41e+03 1.95e+00 bond pdb=" C PRO A 400 " pdb=" N PRO A 401 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.91e+00 ... (remaining 8154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 10675 1.88 - 3.75: 387 3.75 - 5.63: 63 5.63 - 7.51: 17 7.51 - 9.38: 4 Bond angle restraints: 11146 Sorted by residual: angle pdb=" N PRO B 331 " pdb=" CA PRO B 331 " pdb=" CB PRO B 331 " ideal model delta sigma weight residual 103.46 110.27 -6.81 9.30e-01 1.16e+00 5.36e+01 angle pdb=" N PRO B 302 " pdb=" CA PRO B 302 " pdb=" CB PRO B 302 " ideal model delta sigma weight residual 103.51 110.24 -6.73 9.60e-01 1.09e+00 4.91e+01 angle pdb=" N PRO B 345 " pdb=" CA PRO B 345 " pdb=" CB PRO B 345 " ideal model delta sigma weight residual 103.25 110.49 -7.24 1.05e+00 9.07e-01 4.75e+01 angle pdb=" N PRO B 262 " pdb=" CA PRO B 262 " pdb=" CB PRO B 262 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 angle pdb=" N PRO B 732 " pdb=" CA PRO B 732 " pdb=" CB PRO B 732 " ideal model delta sigma weight residual 103.39 110.17 -6.78 1.08e+00 8.57e-01 3.94e+01 ... (remaining 11141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4521 17.95 - 35.90: 343 35.90 - 53.85: 56 53.85 - 71.80: 16 71.80 - 89.75: 6 Dihedral angle restraints: 4942 sinusoidal: 1355 harmonic: 3587 Sorted by residual: dihedral pdb=" CA VAL B 364 " pdb=" C VAL B 364 " pdb=" N VAL B 365 " pdb=" CA VAL B 365 " ideal model delta harmonic sigma weight residual 180.00 145.58 34.42 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA PHE A 180 " pdb=" C PHE A 180 " pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta harmonic sigma weight residual 180.00 145.60 34.40 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA LYS B 281 " pdb=" C LYS B 281 " pdb=" N LYS B 282 " pdb=" CA LYS B 282 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1136 0.051 - 0.101: 247 0.101 - 0.152: 24 0.152 - 0.203: 0 0.203 - 0.254: 6 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA PRO B 331 " pdb=" N PRO B 331 " pdb=" C PRO B 331 " pdb=" CB PRO B 331 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO B 302 " pdb=" N PRO B 302 " pdb=" C PRO B 302 " pdb=" CB PRO B 302 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA PRO B 772 " pdb=" N PRO B 772 " pdb=" C PRO B 772 " pdb=" CB PRO B 772 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1410 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 180 " 0.064 5.00e-02 4.00e+02 9.64e-02 1.49e+01 pdb=" N PRO A 181 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 385 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO B 386 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 386 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 386 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 400 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 401 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " -0.028 5.00e-02 4.00e+02 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 133 2.65 - 3.21: 8929 3.21 - 3.77: 12493 3.77 - 4.34: 15878 4.34 - 4.90: 23816 Nonbonded interactions: 61249 Sorted by model distance: nonbonded pdb=" O SER A 346 " pdb=" ND1 HIS A 351 " model vdw 2.087 3.120 nonbonded pdb=" O GLU B 568 " pdb=" NZ LYS B 659 " model vdw 2.135 3.120 nonbonded pdb=" O VAL A 199 " pdb=" OG SER A 202 " model vdw 2.174 3.040 nonbonded pdb=" O LEU A 133 " pdb=" N VAL A 135 " model vdw 2.201 3.120 nonbonded pdb=" O ARG A 358 " pdb=" OG SER A 361 " model vdw 2.214 3.040 ... (remaining 61244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.200 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 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 : 0.004 0.032 8159 Z= 0.245 Angle : 0.874 9.382 11146 Z= 0.493 Chirality : 0.042 0.254 1413 Planarity : 0.005 0.096 1469 Dihedral : 14.593 89.746 2578 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.38 % Favored : 85.06 % Rotamer: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -5.17 (0.21), residues: 890 helix: -2.52 (0.17), residues: 613 sheet: None (None), residues: 0 loop : -5.38 (0.23), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 343 HIS 0.007 0.001 HIS A 351 PHE 0.019 0.001 PHE A 297 TYR 0.021 0.002 TYR B 498 ARG 0.007 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.7831 (t) cc_final: 0.7583 (t) REVERT: A 107 ILE cc_start: 0.6438 (pt) cc_final: 0.6070 (pt) REVERT: A 118 MET cc_start: 0.3965 (tpt) cc_final: 0.3653 (tpt) REVERT: A 128 LEU cc_start: 0.6937 (mt) cc_final: 0.6434 (mt) REVERT: A 151 LEU cc_start: 0.6727 (tp) cc_final: 0.6315 (tp) REVERT: A 253 TRP cc_start: 0.6033 (m-10) cc_final: 0.5779 (m-10) REVERT: A 291 LYS cc_start: 0.6069 (ttmt) cc_final: 0.5771 (ttmt) REVERT: A 292 ASN cc_start: 0.7909 (t0) cc_final: 0.7653 (t0) REVERT: A 331 LEU cc_start: 0.7969 (tp) cc_final: 0.7701 (tt) REVERT: A 334 GLN cc_start: 0.5620 (tm-30) cc_final: 0.5203 (tm-30) REVERT: A 337 LYS cc_start: 0.7167 (mtmm) cc_final: 0.6882 (ttmm) REVERT: B 354 VAL cc_start: 0.7453 (p) cc_final: 0.6217 (p) REVERT: B 380 SER cc_start: 0.7769 (m) cc_final: 0.7294 (p) REVERT: B 389 MET cc_start: 0.5060 (mtp) cc_final: 0.4819 (mtp) REVERT: B 422 VAL cc_start: 0.7892 (t) cc_final: 0.7685 (p) REVERT: B 427 ARG cc_start: 0.7217 (mmm160) cc_final: 0.7001 (mmm160) REVERT: B 524 MET cc_start: 0.6972 (ttm) cc_final: 0.6608 (ttm) REVERT: B 525 ILE cc_start: 0.8146 (mm) cc_final: 0.7924 (mm) REVERT: B 564 TYR cc_start: 0.5304 (m-10) cc_final: 0.5055 (m-10) REVERT: B 691 ILE cc_start: 0.8153 (mm) cc_final: 0.7921 (mt) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2207 time to fit residues: 76.8910 Evaluate side-chains 244 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 chunk 109 optimal weight: 4.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 228 GLN A 258 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN B 352 ASN B 434 GLN B 513 HIS B 626 GLN B 663 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8159 Z= 0.219 Angle : 0.772 10.828 11146 Z= 0.381 Chirality : 0.039 0.200 1413 Planarity : 0.006 0.096 1469 Dihedral : 5.480 32.919 1264 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.02 % Favored : 87.64 % Rotamer: Outliers : 0.17 % Allowed : 6.00 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -3.01 (0.25), residues: 890 helix: -0.78 (0.19), residues: 619 sheet: None (None), residues: 0 loop : -4.91 (0.29), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 343 HIS 0.006 0.001 HIS A 351 PHE 0.025 0.002 PHE B 417 TYR 0.023 0.002 TYR B 498 ARG 0.005 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.4659 (mmm) cc_final: 0.4156 (mmm) REVERT: A 106 THR cc_start: 0.6883 (p) cc_final: 0.6631 (p) REVERT: A 107 ILE cc_start: 0.6440 (pt) cc_final: 0.5862 (pt) REVERT: A 128 LEU cc_start: 0.6505 (mt) cc_final: 0.6187 (mt) REVERT: A 238 LEU cc_start: 0.5252 (tp) cc_final: 0.4976 (tp) REVERT: A 256 VAL cc_start: 0.7482 (m) cc_final: 0.7113 (p) REVERT: A 257 GLU cc_start: 0.6846 (tm-30) cc_final: 0.6446 (tm-30) REVERT: A 261 ASP cc_start: 0.7034 (m-30) cc_final: 0.6799 (m-30) REVERT: A 265 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6775 (tm-30) REVERT: A 291 LYS cc_start: 0.6668 (ttmt) cc_final: 0.6374 (ttmm) REVERT: A 319 LEU cc_start: 0.6438 (tt) cc_final: 0.6203 (tt) REVERT: A 362 LYS cc_start: 0.6943 (mtmm) cc_final: 0.6645 (mtmm) REVERT: A 404 ARG cc_start: 0.6352 (mmt180) cc_final: 0.6058 (mmt180) REVERT: A 407 MET cc_start: 0.5733 (ptp) cc_final: 0.5386 (ptp) REVERT: B 380 SER cc_start: 0.7715 (m) cc_final: 0.7326 (p) REVERT: B 381 LEU cc_start: 0.7958 (pp) cc_final: 0.7641 (pp) REVERT: B 385 LEU cc_start: 0.7633 (pp) cc_final: 0.7431 (pp) REVERT: B 400 THR cc_start: 0.7617 (p) cc_final: 0.7015 (t) REVERT: B 427 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6892 (mmm160) REVERT: B 524 MET cc_start: 0.6961 (ttm) cc_final: 0.6579 (ttm) REVERT: B 525 ILE cc_start: 0.7778 (mm) cc_final: 0.7546 (mm) REVERT: B 526 LEU cc_start: 0.7774 (mm) cc_final: 0.7335 (mm) REVERT: B 631 LEU cc_start: 0.8130 (mt) cc_final: 0.7877 (mm) REVERT: B 650 MET cc_start: 0.6642 (pmm) cc_final: 0.6271 (pmm) REVERT: B 672 THR cc_start: 0.7804 (p) cc_final: 0.7209 (p) REVERT: B 674 THR cc_start: 0.6986 (p) cc_final: 0.6670 (p) REVERT: B 691 ILE cc_start: 0.8259 (mm) cc_final: 0.8035 (mt) REVERT: B 706 LEU cc_start: 0.7559 (mm) cc_final: 0.7116 (mm) outliers start: 1 outliers final: 1 residues processed: 255 average time/residue: 0.2268 time to fit residues: 74.7254 Evaluate side-chains 236 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 258 GLN ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS B 623 ASN B 626 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8159 Z= 0.275 Angle : 0.796 10.215 11146 Z= 0.400 Chirality : 0.040 0.151 1413 Planarity : 0.006 0.095 1469 Dihedral : 5.465 33.040 1264 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.27 % Favored : 85.62 % Rotamer: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -2.45 (0.26), residues: 890 helix: -0.36 (0.20), residues: 623 sheet: None (None), residues: 0 loop : -4.77 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 74 HIS 0.014 0.002 HIS A 351 PHE 0.024 0.002 PHE A 297 TYR 0.033 0.002 TYR B 498 ARG 0.009 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7968 (m) cc_final: 0.7503 (p) REVERT: A 104 MET cc_start: 0.4674 (mmm) cc_final: 0.4357 (mmm) REVERT: A 106 THR cc_start: 0.6863 (p) cc_final: 0.6583 (p) REVERT: A 107 ILE cc_start: 0.6505 (pt) cc_final: 0.5919 (pt) REVERT: A 220 LYS cc_start: 0.6337 (mmpt) cc_final: 0.6078 (mmpt) REVERT: A 256 VAL cc_start: 0.7442 (m) cc_final: 0.7119 (p) REVERT: A 265 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6647 (tm-30) REVERT: A 291 LYS cc_start: 0.6706 (ttmt) cc_final: 0.6445 (ttmt) REVERT: A 337 LYS cc_start: 0.7168 (mttp) cc_final: 0.6814 (ttmm) REVERT: A 338 GLU cc_start: 0.5781 (mp0) cc_final: 0.5253 (mp0) REVERT: A 404 ARG cc_start: 0.6461 (mmt180) cc_final: 0.6058 (mmt180) REVERT: A 407 MET cc_start: 0.6056 (ptp) cc_final: 0.5845 (ptp) REVERT: B 380 SER cc_start: 0.7844 (m) cc_final: 0.7551 (p) REVERT: B 385 LEU cc_start: 0.7492 (pp) cc_final: 0.5922 (pp) REVERT: B 398 PHE cc_start: 0.7435 (t80) cc_final: 0.6931 (t80) REVERT: B 400 THR cc_start: 0.7742 (p) cc_final: 0.7274 (t) REVERT: B 422 VAL cc_start: 0.7433 (t) cc_final: 0.7029 (p) REVERT: B 426 GLN cc_start: 0.7489 (mt0) cc_final: 0.7220 (mt0) REVERT: B 486 MET cc_start: 0.5063 (mpp) cc_final: 0.4845 (mpp) REVERT: B 524 MET cc_start: 0.6972 (ttm) cc_final: 0.6630 (ttm) REVERT: B 560 ILE cc_start: 0.8310 (pt) cc_final: 0.7992 (pt) REVERT: B 561 LEU cc_start: 0.7733 (mt) cc_final: 0.7419 (mt) REVERT: B 626 GLN cc_start: 0.7262 (tp40) cc_final: 0.6943 (tp40) REVERT: B 650 MET cc_start: 0.6608 (pmm) cc_final: 0.6405 (pmm) REVERT: B 674 THR cc_start: 0.7136 (p) cc_final: 0.6744 (p) REVERT: B 706 LEU cc_start: 0.7575 (mm) cc_final: 0.7105 (mm) outliers start: 1 outliers final: 1 residues processed: 251 average time/residue: 0.2265 time to fit residues: 73.4035 Evaluate side-chains 231 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN B 379 HIS B 392 GLN ** B 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS B 630 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8159 Z= 0.202 Angle : 0.748 8.815 11146 Z= 0.371 Chirality : 0.039 0.143 1413 Planarity : 0.005 0.095 1469 Dihedral : 5.168 32.595 1264 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.02 % Favored : 87.87 % Rotamer: Outliers : 0.33 % Allowed : 4.50 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -1.79 (0.27), residues: 890 helix: 0.21 (0.20), residues: 618 sheet: None (None), residues: 0 loop : -4.63 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.005 0.001 HIS A 351 PHE 0.025 0.002 PHE A 297 TYR 0.022 0.002 TYR B 498 ARG 0.007 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7909 (m) cc_final: 0.7280 (p) REVERT: A 104 MET cc_start: 0.4735 (mmm) cc_final: 0.4510 (mmm) REVERT: A 107 ILE cc_start: 0.6296 (pt) cc_final: 0.6095 (pt) REVERT: A 196 LEU cc_start: 0.6216 (tt) cc_final: 0.5640 (tt) REVERT: A 220 LYS cc_start: 0.6210 (mmpt) cc_final: 0.5995 (mmpt) REVERT: A 404 ARG cc_start: 0.6318 (mmt180) cc_final: 0.5931 (mmm160) REVERT: A 407 MET cc_start: 0.5889 (ptp) cc_final: 0.5613 (ptp) REVERT: B 400 THR cc_start: 0.7646 (p) cc_final: 0.7277 (t) REVERT: B 426 GLN cc_start: 0.7372 (mt0) cc_final: 0.7073 (mt0) REVERT: B 524 MET cc_start: 0.6853 (ttm) cc_final: 0.6615 (ttm) REVERT: B 525 ILE cc_start: 0.7602 (mm) cc_final: 0.7398 (mm) REVERT: B 526 LEU cc_start: 0.7594 (mt) cc_final: 0.7288 (mt) REVERT: B 626 GLN cc_start: 0.7136 (tp40) cc_final: 0.6796 (tp40) REVERT: B 672 THR cc_start: 0.7697 (p) cc_final: 0.7149 (p) REVERT: B 674 THR cc_start: 0.7110 (p) cc_final: 0.6599 (p) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.2269 time to fit residues: 73.1789 Evaluate side-chains 238 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 144 GLN A 258 GLN A 357 GLN B 513 HIS B 623 ASN B 626 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8159 Z= 0.235 Angle : 0.769 8.810 11146 Z= 0.382 Chirality : 0.039 0.160 1413 Planarity : 0.005 0.097 1469 Dihedral : 5.218 31.765 1264 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.82 % Favored : 86.07 % Rotamer: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.28), residues: 890 helix: 0.32 (0.20), residues: 618 sheet: None (None), residues: 0 loop : -4.60 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 74 HIS 0.009 0.001 HIS A 351 PHE 0.030 0.002 PHE B 417 TYR 0.028 0.002 TYR B 498 ARG 0.008 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7964 (m) cc_final: 0.7661 (m) REVERT: A 106 THR cc_start: 0.6780 (p) cc_final: 0.6534 (p) REVERT: A 107 ILE cc_start: 0.6407 (pt) cc_final: 0.6145 (pt) REVERT: A 255 LEU cc_start: 0.7595 (tt) cc_final: 0.7366 (tp) REVERT: A 258 GLN cc_start: 0.6474 (OUTLIER) cc_final: 0.5847 (pp30) REVERT: A 291 LYS cc_start: 0.6295 (ttmt) cc_final: 0.5854 (ttmt) REVERT: A 334 GLN cc_start: 0.5462 (tm-30) cc_final: 0.4997 (tm-30) REVERT: A 337 LYS cc_start: 0.7132 (mttp) cc_final: 0.6904 (ttmm) REVERT: A 338 GLU cc_start: 0.5703 (mp0) cc_final: 0.5239 (mp0) REVERT: A 384 LEU cc_start: 0.7251 (pp) cc_final: 0.6992 (pp) REVERT: A 404 ARG cc_start: 0.6341 (mmt180) cc_final: 0.6098 (mmt180) REVERT: A 407 MET cc_start: 0.6022 (ptp) cc_final: 0.5664 (ptp) REVERT: B 385 LEU cc_start: 0.7058 (pp) cc_final: 0.5025 (pp) REVERT: B 398 PHE cc_start: 0.7118 (t80) cc_final: 0.6877 (t80) REVERT: B 400 THR cc_start: 0.7882 (p) cc_final: 0.7432 (t) REVERT: B 404 LEU cc_start: 0.7189 (tp) cc_final: 0.6969 (tt) REVERT: B 426 GLN cc_start: 0.7376 (mt0) cc_final: 0.7133 (mt0) REVERT: B 526 LEU cc_start: 0.7578 (mt) cc_final: 0.7359 (mt) REVERT: B 626 GLN cc_start: 0.7139 (tp-100) cc_final: 0.6884 (tp-100) REVERT: B 630 GLN cc_start: 0.7785 (mm110) cc_final: 0.6770 (mm-40) REVERT: B 674 THR cc_start: 0.7127 (p) cc_final: 0.6681 (p) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2232 time to fit residues: 71.7509 Evaluate side-chains 233 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 0.0050 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8159 Z= 0.208 Angle : 0.742 7.782 11146 Z= 0.366 Chirality : 0.039 0.187 1413 Planarity : 0.005 0.101 1469 Dihedral : 5.055 30.263 1264 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.02 % Favored : 87.87 % Rotamer: Outliers : 0.17 % Allowed : 2.50 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -1.41 (0.28), residues: 890 helix: 0.45 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -4.46 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 87 HIS 0.005 0.001 HIS A 351 PHE 0.024 0.002 PHE A 297 TYR 0.022 0.001 TYR B 498 ARG 0.008 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.8026 (m) cc_final: 0.7457 (p) REVERT: A 107 ILE cc_start: 0.6255 (pt) cc_final: 0.5893 (pt) REVERT: A 182 GLN cc_start: 0.5868 (tm-30) cc_final: 0.5619 (tm-30) REVERT: A 291 LYS cc_start: 0.6417 (ttmt) cc_final: 0.5940 (ttmt) REVERT: A 383 LEU cc_start: 0.6291 (tp) cc_final: 0.6058 (tp) REVERT: A 384 LEU cc_start: 0.7151 (pp) cc_final: 0.6825 (pp) REVERT: A 404 ARG cc_start: 0.6215 (mmt180) cc_final: 0.5930 (mmt180) REVERT: A 407 MET cc_start: 0.5907 (ptp) cc_final: 0.5668 (ptp) REVERT: B 385 LEU cc_start: 0.6847 (pp) cc_final: 0.4937 (pp) REVERT: B 400 THR cc_start: 0.7733 (p) cc_final: 0.7308 (t) REVERT: B 404 LEU cc_start: 0.7340 (tp) cc_final: 0.7005 (tt) REVERT: B 426 GLN cc_start: 0.7325 (mt0) cc_final: 0.7091 (mt0) REVERT: B 427 ARG cc_start: 0.6829 (mmm160) cc_final: 0.6224 (mmm160) REVERT: B 525 ILE cc_start: 0.7561 (mm) cc_final: 0.7314 (mm) REVERT: B 549 ASN cc_start: 0.7555 (t0) cc_final: 0.7351 (t0) REVERT: B 564 TYR cc_start: 0.5358 (m-10) cc_final: 0.5104 (m-10) REVERT: B 630 GLN cc_start: 0.7822 (mm110) cc_final: 0.6869 (mm-40) REVERT: B 631 LEU cc_start: 0.7981 (mt) cc_final: 0.7715 (mm) REVERT: B 672 THR cc_start: 0.7606 (p) cc_final: 0.6995 (p) REVERT: B 674 THR cc_start: 0.7108 (p) cc_final: 0.6600 (p) outliers start: 1 outliers final: 1 residues processed: 251 average time/residue: 0.2237 time to fit residues: 73.0029 Evaluate side-chains 235 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 258 GLN A 356 GLN B 513 HIS B 623 ASN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8159 Z= 0.224 Angle : 0.768 7.853 11146 Z= 0.381 Chirality : 0.040 0.153 1413 Planarity : 0.005 0.106 1469 Dihedral : 5.067 30.819 1264 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.92 % Favored : 86.97 % Rotamer: Outliers : 0.17 % Allowed : 1.33 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.37 (0.28), residues: 890 helix: 0.48 (0.20), residues: 623 sheet: None (None), residues: 0 loop : -4.43 (0.33), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.006 0.001 HIS A 351 PHE 0.038 0.002 PHE A 297 TYR 0.022 0.001 TYR B 498 ARG 0.005 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.8006 (m) cc_final: 0.7390 (p) REVERT: A 106 THR cc_start: 0.6580 (p) cc_final: 0.6328 (p) REVERT: A 107 ILE cc_start: 0.6325 (pt) cc_final: 0.5908 (pt) REVERT: A 258 GLN cc_start: 0.6370 (OUTLIER) cc_final: 0.5924 (pp30) REVERT: A 334 GLN cc_start: 0.5581 (tm-30) cc_final: 0.5158 (tm-30) REVERT: A 337 LYS cc_start: 0.7182 (mttp) cc_final: 0.6925 (ttmm) REVERT: A 338 GLU cc_start: 0.5530 (mp0) cc_final: 0.5138 (mp0) REVERT: A 383 LEU cc_start: 0.6333 (tp) cc_final: 0.6003 (tp) REVERT: A 384 LEU cc_start: 0.7271 (pp) cc_final: 0.6917 (pp) REVERT: A 403 ARG cc_start: 0.6065 (tpp80) cc_final: 0.5524 (tpp80) REVERT: A 404 ARG cc_start: 0.6246 (mmt180) cc_final: 0.5718 (tpt170) REVERT: A 407 MET cc_start: 0.5890 (ptp) cc_final: 0.5514 (ptp) REVERT: B 400 THR cc_start: 0.7679 (p) cc_final: 0.7298 (t) REVERT: B 404 LEU cc_start: 0.7421 (tp) cc_final: 0.7157 (tt) REVERT: B 426 GLN cc_start: 0.7320 (mt0) cc_final: 0.7114 (mt0) REVERT: B 427 ARG cc_start: 0.6648 (mmm160) cc_final: 0.6084 (mmm160) REVERT: B 525 ILE cc_start: 0.7729 (mm) cc_final: 0.7374 (mm) REVERT: B 564 TYR cc_start: 0.5381 (m-10) cc_final: 0.5037 (m-10) REVERT: B 630 GLN cc_start: 0.7826 (mm110) cc_final: 0.6712 (mm-40) REVERT: B 672 THR cc_start: 0.7641 (p) cc_final: 0.7027 (p) REVERT: B 674 THR cc_start: 0.7195 (p) cc_final: 0.6759 (p) outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.2229 time to fit residues: 71.4920 Evaluate side-chains 247 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.0020 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS B 688 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8159 Z= 0.293 Angle : 0.811 8.331 11146 Z= 0.409 Chirality : 0.042 0.187 1413 Planarity : 0.006 0.107 1469 Dihedral : 5.313 31.262 1264 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.83 % Favored : 85.17 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.12 % 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: -1.67 (0.28), residues: 890 helix: 0.20 (0.20), residues: 629 sheet: None (None), residues: 0 loop : -4.50 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 74 HIS 0.011 0.002 HIS A 351 PHE 0.029 0.002 PHE A 297 TYR 0.048 0.003 TYR B 564 ARG 0.007 0.001 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 THR cc_start: 0.6668 (p) cc_final: 0.6387 (p) REVERT: A 107 ILE cc_start: 0.6409 (pt) cc_final: 0.6056 (pt) REVERT: A 155 THR cc_start: 0.6941 (p) cc_final: 0.6693 (p) REVERT: A 182 GLN cc_start: 0.5732 (tm-30) cc_final: 0.5496 (tm-30) REVERT: A 258 GLN cc_start: 0.6579 (pp30) cc_final: 0.6027 (pp30) REVERT: A 291 LYS cc_start: 0.6873 (ttmt) cc_final: 0.6498 (ttmm) REVERT: A 337 LYS cc_start: 0.7191 (mttp) cc_final: 0.6963 (ttmm) REVERT: A 338 GLU cc_start: 0.5665 (mp0) cc_final: 0.5446 (mp0) REVERT: A 383 LEU cc_start: 0.6522 (tp) cc_final: 0.6204 (tp) REVERT: A 384 LEU cc_start: 0.7328 (pp) cc_final: 0.6855 (pp) REVERT: A 403 ARG cc_start: 0.6159 (tpp80) cc_final: 0.5607 (tpp80) REVERT: A 404 ARG cc_start: 0.6302 (mmt180) cc_final: 0.5764 (tpt170) REVERT: A 407 MET cc_start: 0.6013 (ptp) cc_final: 0.5706 (ptp) REVERT: B 400 THR cc_start: 0.7676 (p) cc_final: 0.7226 (t) REVERT: B 404 LEU cc_start: 0.7642 (tp) cc_final: 0.7300 (tt) REVERT: B 549 ASN cc_start: 0.7823 (t0) cc_final: 0.7483 (t0) REVERT: B 630 GLN cc_start: 0.7773 (mm110) cc_final: 0.7115 (mm-40) REVERT: B 672 THR cc_start: 0.7849 (p) cc_final: 0.7205 (p) REVERT: B 674 THR cc_start: 0.7225 (p) cc_final: 0.6804 (p) REVERT: B 675 MET cc_start: 0.5995 (mtt) cc_final: 0.5484 (mtt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2267 time to fit residues: 73.0226 Evaluate side-chains 238 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS B 623 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8159 Z= 0.240 Angle : 0.792 9.678 11146 Z= 0.394 Chirality : 0.041 0.165 1413 Planarity : 0.006 0.113 1469 Dihedral : 5.196 31.407 1264 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.51 (0.28), residues: 890 helix: 0.36 (0.20), residues: 623 sheet: None (None), residues: 0 loop : -4.46 (0.32), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 74 HIS 0.007 0.001 HIS A 351 PHE 0.015 0.002 PHE B 398 TYR 0.038 0.002 TYR B 564 ARG 0.009 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 THR cc_start: 0.6565 (p) cc_final: 0.6303 (p) REVERT: A 107 ILE cc_start: 0.6302 (pt) cc_final: 0.5941 (pt) REVERT: A 155 THR cc_start: 0.6927 (p) cc_final: 0.6687 (p) REVERT: A 182 GLN cc_start: 0.5893 (tm-30) cc_final: 0.5555 (tm-30) REVERT: A 220 LYS cc_start: 0.5936 (mmtp) cc_final: 0.5696 (tppp) REVERT: A 258 GLN cc_start: 0.6532 (pp30) cc_final: 0.6171 (pp30) REVERT: A 261 ASP cc_start: 0.6841 (m-30) cc_final: 0.6246 (m-30) REVERT: A 291 LYS cc_start: 0.6932 (ttmt) cc_final: 0.6488 (ttmm) REVERT: A 337 LYS cc_start: 0.7192 (mttp) cc_final: 0.6889 (ttmm) REVERT: A 384 LEU cc_start: 0.7332 (pp) cc_final: 0.7044 (pp) REVERT: A 403 ARG cc_start: 0.6111 (tpp80) cc_final: 0.5553 (tpp80) REVERT: A 404 ARG cc_start: 0.6267 (mmt180) cc_final: 0.5734 (tpt170) REVERT: A 407 MET cc_start: 0.5839 (ptp) cc_final: 0.5525 (ptp) REVERT: B 385 LEU cc_start: 0.6632 (pp) cc_final: 0.6161 (pp) REVERT: B 398 PHE cc_start: 0.6853 (t80) cc_final: 0.6563 (t80) REVERT: B 400 THR cc_start: 0.7695 (p) cc_final: 0.7286 (t) REVERT: B 404 LEU cc_start: 0.7542 (tp) cc_final: 0.7210 (tt) REVERT: B 427 ARG cc_start: 0.6657 (mmm160) cc_final: 0.6128 (mmm160) REVERT: B 486 MET cc_start: 0.4896 (mpp) cc_final: 0.4539 (mpp) REVERT: B 549 ASN cc_start: 0.7734 (t0) cc_final: 0.7300 (t0) REVERT: B 630 GLN cc_start: 0.7735 (mm110) cc_final: 0.7127 (mm-40) REVERT: B 674 THR cc_start: 0.7098 (p) cc_final: 0.6763 (p) REVERT: B 675 MET cc_start: 0.5857 (mtt) cc_final: 0.5454 (mtt) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2237 time to fit residues: 72.0243 Evaluate side-chains 239 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0030 chunk 79 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 513 HIS B 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8159 Z= 0.209 Angle : 0.790 13.021 11146 Z= 0.388 Chirality : 0.040 0.190 1413 Planarity : 0.006 0.115 1469 Dihedral : 5.108 31.524 1264 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.58 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.36 (0.28), residues: 890 helix: 0.45 (0.20), residues: 629 sheet: None (None), residues: 0 loop : -4.44 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 343 HIS 0.005 0.001 HIS B 714 PHE 0.021 0.002 PHE A 297 TYR 0.035 0.002 TYR B 564 ARG 0.020 0.001 ARG B 554 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 VAL cc_start: 0.7957 (m) cc_final: 0.7412 (p) REVERT: A 106 THR cc_start: 0.6557 (p) cc_final: 0.6243 (p) REVERT: A 107 ILE cc_start: 0.6172 (pt) cc_final: 0.5823 (pt) REVERT: A 155 THR cc_start: 0.6833 (p) cc_final: 0.6566 (p) REVERT: A 182 GLN cc_start: 0.6183 (tm-30) cc_final: 0.5872 (tm-30) REVERT: A 194 ARG cc_start: 0.6401 (mmp-170) cc_final: 0.5956 (mmp80) REVERT: A 258 GLN cc_start: 0.6280 (pp30) cc_final: 0.5900 (pp30) REVERT: A 291 LYS cc_start: 0.6911 (ttmt) cc_final: 0.6689 (ttmm) REVERT: A 383 LEU cc_start: 0.6234 (tp) cc_final: 0.5818 (tp) REVERT: A 384 LEU cc_start: 0.7101 (pp) cc_final: 0.6580 (pp) REVERT: A 403 ARG cc_start: 0.6110 (tpp80) cc_final: 0.5564 (tpp80) REVERT: A 404 ARG cc_start: 0.6202 (mmt180) cc_final: 0.5669 (tpt170) REVERT: A 407 MET cc_start: 0.5667 (ptp) cc_final: 0.5326 (ptp) REVERT: B 385 LEU cc_start: 0.6635 (pp) cc_final: 0.6150 (pp) REVERT: B 398 PHE cc_start: 0.6755 (t80) cc_final: 0.6486 (t80) REVERT: B 400 THR cc_start: 0.7676 (p) cc_final: 0.7284 (t) REVERT: B 404 LEU cc_start: 0.7475 (tp) cc_final: 0.7116 (tt) REVERT: B 427 ARG cc_start: 0.6655 (mmm160) cc_final: 0.6187 (mmm160) REVERT: B 486 MET cc_start: 0.4670 (mpp) cc_final: 0.4366 (mpp) REVERT: B 524 MET cc_start: 0.6635 (mmm) cc_final: 0.6251 (mmm) REVERT: B 630 GLN cc_start: 0.7691 (mm110) cc_final: 0.6911 (mm-40) REVERT: B 631 LEU cc_start: 0.7917 (mt) cc_final: 0.7684 (mm) REVERT: B 641 LEU cc_start: 0.7186 (tp) cc_final: 0.6948 (tp) REVERT: B 672 THR cc_start: 0.7702 (p) cc_final: 0.7095 (p) REVERT: B 674 THR cc_start: 0.7052 (p) cc_final: 0.6685 (p) REVERT: B 675 MET cc_start: 0.5760 (mtt) cc_final: 0.5398 (mtt) REVERT: B 702 ILE cc_start: 0.7908 (pt) cc_final: 0.7596 (tt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2295 time to fit residues: 72.9170 Evaluate side-chains 242 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 5 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 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 GLN B 513 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.124091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.099071 restraints weight = 22213.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101910 restraints weight = 15663.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.104120 restraints weight = 11864.062| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8159 Z= 0.197 Angle : 0.762 10.268 11146 Z= 0.376 Chirality : 0.039 0.174 1413 Planarity : 0.006 0.116 1469 Dihedral : 4.934 30.452 1264 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.12 % Favored : 88.76 % Rotamer: Outliers : 0.17 % Allowed : 0.33 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.05 (0.29), residues: 890 helix: 0.75 (0.21), residues: 621 sheet: None (None), residues: 0 loop : -4.36 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 343 HIS 0.004 0.001 HIS B 714 PHE 0.021 0.002 PHE A 213 TYR 0.032 0.002 TYR B 564 ARG 0.018 0.001 ARG B 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2032.01 seconds wall clock time: 36 minutes 35.43 seconds (2195.43 seconds total)