Starting phenix.real_space_refine on Sun Sep 29 15:15:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nbx_12262/09_2024/7nbx_12262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nbx_12262/09_2024/7nbx_12262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nbx_12262/09_2024/7nbx_12262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nbx_12262/09_2024/7nbx_12262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nbx_12262/09_2024/7nbx_12262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nbx_12262/09_2024/7nbx_12262.cif" } resolution = 4.8 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= 0.004 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7251 2.51 5 N 1968 2.21 5 O 2257 1.98 5 H 11129 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22637 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11784 Classifications: {'peptide': 761} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 5307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5307 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 11, 'TRANS': 345} Chain breaks: 1 Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 817 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3459 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1270 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Time building chain proxies: 11.19, per 1000 atoms: 0.49 Number of scatterers: 22637 At special positions: 0 Unit cell: (117.7, 141.24, 103.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2257 8.00 N 1968 7.00 C 7251 6.00 H 11129 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 665 " distance=2.03 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: 6.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 18 sheets defined 22.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.713A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.634A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.633A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.924A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 removed outlier: 4.414A pdb=" N TRP A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.914A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 3.975A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.674A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.538A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.875A pdb=" N GLY D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.773A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.717A pdb=" N MET D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.669A pdb=" N ILE E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.641A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.064A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 8.018A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 355 removed outlier: 6.776A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.943A pdb=" N GLY A 443 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL A 483 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 630 " --> pdb=" O GLU A 717 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 636 " --> pdb=" O MET A 711 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 672 removed outlier: 3.966A pdb=" N ALA A 672 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 703 " --> pdb=" O ALA A 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.530A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB2, first strand: chain 'B' and resid 117 through 118 removed outlier: 6.688A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.413A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.784A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.537A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 332 removed outlier: 3.927A pdb=" N VAL B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 338 " --> pdb=" O VAL B 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 345 through 348 removed outlier: 3.757A pdb=" N GLN B 360 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 33 through 35 456 hydrogen bonds defined for protein. 1272 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: 7.83 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11129 1.03 - 1.22: 4 1.22 - 1.42: 5068 1.42 - 1.62: 6621 1.62 - 1.82: 62 Bond restraints: 22884 Sorted by residual: bond pdb=" N PHE A 517 " pdb=" CA PHE A 517 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.04e-02 9.25e+03 6.10e+00 bond pdb=" CA ASN E 106 " pdb=" CB ASN E 106 " ideal model delta sigma weight residual 1.527 1.496 0.030 1.27e-02 6.20e+03 5.74e+00 bond pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 1.536 1.505 0.031 1.46e-02 4.69e+03 4.62e+00 bond pdb=" C GLY D 65 " pdb=" N PRO D 66 " ideal model delta sigma weight residual 1.337 1.313 0.024 1.24e-02 6.50e+03 3.74e+00 bond pdb=" CB TRP B 143 " pdb=" CG TRP B 143 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.45e+00 ... (remaining 22879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 39467 2.02 - 4.03: 1580 4.03 - 6.05: 108 6.05 - 8.07: 11 8.07 - 10.09: 3 Bond angle restraints: 41169 Sorted by residual: angle pdb=" N GLY B 211 " pdb=" CA GLY B 211 " pdb=" C GLY B 211 " ideal model delta sigma weight residual 111.85 104.09 7.76 1.06e+00 8.90e-01 5.37e+01 angle pdb=" C LEU B 152 " pdb=" N SER B 153 " pdb=" CA SER B 153 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N VAL D 192 " pdb=" CA VAL D 192 " pdb=" CB VAL D 192 " ideal model delta sigma weight residual 111.64 107.99 3.65 8.20e-01 1.49e+00 1.98e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" C ASN A 448 " ideal model delta sigma weight residual 110.44 105.23 5.21 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N ASN E 41 " pdb=" CA ASN E 41 " pdb=" C ASN E 41 " ideal model delta sigma weight residual 114.56 109.19 5.37 1.27e+00 6.20e-01 1.79e+01 ... (remaining 41164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9307 17.75 - 35.49: 1116 35.49 - 53.24: 279 53.24 - 70.99: 112 70.99 - 88.73: 34 Dihedral angle restraints: 10848 sinusoidal: 5851 harmonic: 4997 Sorted by residual: dihedral pdb=" CA SER A 557 " pdb=" C SER A 557 " pdb=" N THR A 558 " pdb=" CA THR A 558 " ideal model delta harmonic sigma weight residual 180.00 130.70 49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N SER B 153 " pdb=" CA SER B 153 " ideal model delta harmonic sigma weight residual 180.00 -135.51 -44.49 0 5.00e+00 4.00e-02 7.92e+01 dihedral pdb=" CA PRO B 371 " pdb=" C PRO B 371 " pdb=" N VAL B 372 " pdb=" CA VAL B 372 " ideal model delta harmonic sigma weight residual 180.00 146.12 33.88 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 10845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1219 0.048 - 0.095: 413 0.095 - 0.143: 103 0.143 - 0.191: 13 0.191 - 0.238: 2 Chirality restraints: 1750 Sorted by residual: chirality pdb=" CG LEU A 450 " pdb=" CB LEU A 450 " pdb=" CD1 LEU A 450 " pdb=" CD2 LEU A 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 505 " pdb=" CA THR A 505 " pdb=" OG1 THR A 505 " pdb=" CG2 THR A 505 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 1747 not shown) Planarity restraints: 3509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 370 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO B 371 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 555 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO A 556 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 374 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ALA B 374 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA B 374 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 375 " -0.015 2.00e-02 2.50e+03 ... (remaining 3506 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2542 2.22 - 2.82: 50800 2.82 - 3.41: 60149 3.41 - 4.01: 78690 4.01 - 4.60: 115940 Nonbonded interactions: 308121 Sorted by model distance: nonbonded pdb=" H SER A 269 " pdb=" O VAL A 335 " model vdw 1.626 2.450 nonbonded pdb=" O MET A 539 " pdb="HD21 ASN A 563 " model vdw 1.637 2.450 nonbonded pdb=" O THR A 190 " pdb=" H ILE A 194 " model vdw 1.658 2.450 nonbonded pdb=" OD2 ASP A 410 " pdb=" H THR E 61 " model vdw 1.658 2.450 nonbonded pdb=" O SER C 73 " pdb=" HG1 THR D 161 " model vdw 1.661 2.450 ... (remaining 308116 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=0.00 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.370 Extract box with map and model: 0.870 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 48.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.008 0.062 11755 Z= 0.513 Angle : 1.043 10.086 15976 Z= 0.619 Chirality : 0.050 0.238 1750 Planarity : 0.006 0.085 2102 Dihedral : 15.897 88.734 4252 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.25 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -4.49 (0.18), residues: 1461 helix: -2.41 (0.22), residues: 283 sheet: -2.37 (0.22), residues: 378 loop : -3.62 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 376 HIS 0.011 0.003 HIS A 533 PHE 0.024 0.002 PHE A 565 TYR 0.020 0.003 TYR A 255 ARG 0.007 0.001 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.861 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: 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: 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 241 ASP cc_start: 0.9127 (m-30) cc_final: 0.8801 (m-30) REVERT: A 503 ASP cc_start: 0.8686 (t0) cc_final: 0.8366 (m-30) REVERT: A 523 ASN cc_start: 0.8839 (m110) cc_final: 0.8395 (m-40) REVERT: A 652 PHE cc_start: 0.8008 (m-80) cc_final: 0.7754 (m-10) REVERT: A 671 LYS cc_start: 0.8882 (pttm) cc_final: 0.8488 (ptpp) REVERT: B 165 HIS cc_start: 0.8274 (t-90) cc_final: 0.7677 (t-90) REVERT: B 367 PHE cc_start: 0.8991 (m-80) cc_final: 0.8713 (m-80) REVERT: D 34 GLU cc_start: 0.9492 (mp0) cc_final: 0.9188 (pm20) REVERT: D 109 MET cc_start: 0.9241 (mmm) cc_final: 0.8814 (mtp) REVERT: D 148 SER cc_start: 0.9580 (m) cc_final: 0.9369 (p) REVERT: D 183 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8840 (tt0) REVERT: D 219 GLU cc_start: 0.8814 (tp30) cc_final: 0.8599 (tp30) REVERT: E 36 ASN cc_start: 0.9345 (m-40) cc_final: 0.8703 (t0) REVERT: E 50 MET cc_start: 0.8702 (mtp) cc_final: 0.8082 (mtp) REVERT: E 107 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8963 (mmtp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.4465 time to fit residues: 101.5236 Evaluate side-chains 113 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 170 GLN A 286 GLN A 323 GLN A 411 GLN A 441 GLN A 506 ASN A 523 ASN A 540 GLN A 561 GLN A 801 GLN A 805 ASN B 40 ASN B 70 ASN B 85 ASN B 130 GLN B 144 GLN B 170 GLN B 319 GLN B 360 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 69 GLN D 82 ASN E 36 ASN E 53 GLN E 54 GLN E 103 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11755 Z= 0.229 Angle : 0.686 6.144 15976 Z= 0.378 Chirality : 0.044 0.153 1750 Planarity : 0.005 0.072 2102 Dihedral : 7.570 45.008 1615 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.88 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.62 (0.19), residues: 1461 helix: -1.02 (0.26), residues: 300 sheet: -2.18 (0.22), residues: 405 loop : -3.18 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 546 HIS 0.006 0.001 HIS A 533 PHE 0.017 0.001 PHE D 95 TYR 0.016 0.002 TYR D 177 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.041 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: 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: 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 369 MET cc_start: 0.9262 (mmt) cc_final: 0.9021 (mmt) REVERT: A 387 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8807 (mt-10) REVERT: A 503 ASP cc_start: 0.8655 (t0) cc_final: 0.8412 (m-30) REVERT: B 165 HIS cc_start: 0.8334 (t-90) cc_final: 0.7737 (t-90) REVERT: B 369 THR cc_start: 0.9798 (p) cc_final: 0.9548 (t) REVERT: D 34 GLU cc_start: 0.9495 (mp0) cc_final: 0.9172 (pm20) REVERT: D 109 MET cc_start: 0.9202 (mmm) cc_final: 0.8709 (mtp) REVERT: D 178 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8775 (mm-30) REVERT: D 201 MET cc_start: 0.9309 (mtp) cc_final: 0.8831 (mtp) REVERT: D 219 GLU cc_start: 0.8836 (tp30) cc_final: 0.8565 (tp30) REVERT: E 50 MET cc_start: 0.8830 (mtp) cc_final: 0.8285 (mtp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.4157 time to fit residues: 88.9132 Evaluate side-chains 115 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 403 GLN B 324 HIS ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN E 52 GLN E 83 HIS E 96 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11755 Z= 0.276 Angle : 0.653 6.566 15976 Z= 0.361 Chirality : 0.043 0.173 1750 Planarity : 0.004 0.068 2102 Dihedral : 6.870 41.632 1615 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.43 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.30 (0.20), residues: 1461 helix: -0.51 (0.27), residues: 299 sheet: -2.00 (0.22), residues: 410 loop : -3.09 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 376 HIS 0.008 0.002 HIS B 347 PHE 0.015 0.001 PHE D 95 TYR 0.018 0.002 TYR A 504 ARG 0.006 0.000 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.932 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.9471 (mmt) cc_final: 0.9113 (mmt) REVERT: A 387 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8874 (mt-10) REVERT: A 503 ASP cc_start: 0.8677 (t0) cc_final: 0.8382 (m-30) REVERT: A 652 PHE cc_start: 0.7896 (m-80) cc_final: 0.7500 (m-10) REVERT: A 671 LYS cc_start: 0.8792 (pttm) cc_final: 0.8349 (ptpp) REVERT: B 165 HIS cc_start: 0.8341 (t-90) cc_final: 0.7933 (t70) REVERT: B 369 THR cc_start: 0.9827 (p) cc_final: 0.9503 (t) REVERT: C 81 ASP cc_start: 0.8558 (t0) cc_final: 0.8335 (t0) REVERT: D 34 GLU cc_start: 0.9485 (mp0) cc_final: 0.9164 (pm20) REVERT: D 201 MET cc_start: 0.9390 (mtp) cc_final: 0.8970 (mtp) REVERT: D 219 GLU cc_start: 0.8796 (tp30) cc_final: 0.8156 (tp30) REVERT: E 36 ASN cc_start: 0.9445 (m110) cc_final: 0.8683 (m-40) REVERT: E 50 MET cc_start: 0.8982 (mtp) cc_final: 0.8446 (mtp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.4212 time to fit residues: 85.6908 Evaluate side-chains 115 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 11755 Z= 0.351 Angle : 0.683 6.581 15976 Z= 0.380 Chirality : 0.043 0.159 1750 Planarity : 0.005 0.074 2102 Dihedral : 6.692 39.662 1615 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.69 % Favored : 86.17 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.38 (0.20), residues: 1461 helix: -0.74 (0.27), residues: 299 sheet: -1.94 (0.22), residues: 415 loop : -3.13 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 376 HIS 0.008 0.002 HIS A 533 PHE 0.020 0.002 PHE A 238 TYR 0.016 0.002 TYR D 185 ARG 0.008 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.854 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: 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: 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 503 ASP cc_start: 0.8813 (t0) cc_final: 0.8340 (m-30) REVERT: B 369 THR cc_start: 0.9847 (p) cc_final: 0.9550 (t) REVERT: C 81 ASP cc_start: 0.8649 (t0) cc_final: 0.8400 (t0) REVERT: D 34 GLU cc_start: 0.9452 (mp0) cc_final: 0.9138 (pm20) REVERT: D 42 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8860 (mmmm) REVERT: D 109 MET cc_start: 0.9361 (mmm) cc_final: 0.8830 (ttt) REVERT: D 178 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8518 (mm-30) REVERT: E 36 ASN cc_start: 0.9484 (m110) cc_final: 0.8674 (t0) REVERT: E 50 MET cc_start: 0.9072 (mtp) cc_final: 0.8392 (mtp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.4409 time to fit residues: 86.7491 Evaluate side-chains 112 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11755 Z= 0.225 Angle : 0.591 6.458 15976 Z= 0.325 Chirality : 0.042 0.150 1750 Planarity : 0.004 0.069 2102 Dihedral : 6.152 36.640 1615 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.47 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.00 (0.21), residues: 1461 helix: -0.14 (0.28), residues: 304 sheet: -1.79 (0.23), residues: 409 loop : -2.99 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 376 HIS 0.012 0.002 HIS A 533 PHE 0.012 0.001 PHE D 95 TYR 0.016 0.001 TYR A 754 ARG 0.005 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.761 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: 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: 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 369 MET cc_start: 0.9586 (mmt) cc_final: 0.9205 (mmt) REVERT: A 503 ASP cc_start: 0.8800 (t0) cc_final: 0.8428 (m-30) REVERT: C 81 ASP cc_start: 0.8689 (t0) cc_final: 0.8454 (t0) REVERT: D 34 GLU cc_start: 0.9412 (mp0) cc_final: 0.9107 (pm20) REVERT: D 42 LYS cc_start: 0.9288 (mmtt) cc_final: 0.8842 (mmmm) REVERT: D 74 ASP cc_start: 0.9228 (m-30) cc_final: 0.9004 (m-30) REVERT: D 178 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 208 THR cc_start: 0.8446 (m) cc_final: 0.8169 (p) REVERT: E 36 ASN cc_start: 0.9490 (m110) cc_final: 0.9274 (m-40) REVERT: E 50 MET cc_start: 0.9038 (mtp) cc_final: 0.8549 (mtp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.4605 time to fit residues: 94.8637 Evaluate side-chains 119 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11755 Z= 0.295 Angle : 0.625 6.256 15976 Z= 0.346 Chirality : 0.042 0.149 1750 Planarity : 0.005 0.071 2102 Dihedral : 6.123 35.146 1615 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.53 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.08 (0.20), residues: 1461 helix: -0.39 (0.28), residues: 306 sheet: -1.66 (0.24), residues: 396 loop : -3.06 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 376 HIS 0.013 0.002 HIS A 533 PHE 0.023 0.001 PHE D 95 TYR 0.014 0.002 TYR A 416 ARG 0.006 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.946 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 ASP cc_start: 0.8842 (t0) cc_final: 0.8405 (m-30) REVERT: A 615 THR cc_start: 0.8418 (m) cc_final: 0.8212 (m) REVERT: B 270 LEU cc_start: 0.9056 (mt) cc_final: 0.8386 (mt) REVERT: C 81 ASP cc_start: 0.8725 (t0) cc_final: 0.8487 (t0) REVERT: D 34 GLU cc_start: 0.9416 (mp0) cc_final: 0.9127 (pm20) REVERT: D 42 LYS cc_start: 0.9339 (mmtt) cc_final: 0.8905 (mmmm) REVERT: D 178 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8494 (mm-30) REVERT: E 36 ASN cc_start: 0.9501 (m110) cc_final: 0.8671 (t0) REVERT: E 50 MET cc_start: 0.9066 (mtp) cc_final: 0.8628 (mtp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4221 time to fit residues: 83.4198 Evaluate side-chains 111 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 139 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 HIS A 805 ASN D 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11755 Z= 0.142 Angle : 0.543 5.501 15976 Z= 0.293 Chirality : 0.043 0.152 1750 Planarity : 0.004 0.062 2102 Dihedral : 5.652 33.750 1615 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.47 (0.21), residues: 1461 helix: 0.57 (0.30), residues: 301 sheet: -1.49 (0.23), residues: 400 loop : -2.73 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 376 HIS 0.009 0.001 HIS A 533 PHE 0.016 0.001 PHE A 648 TYR 0.013 0.001 TYR A 504 ARG 0.003 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.953 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 ASP cc_start: 0.8705 (t0) cc_final: 0.8415 (m-30) REVERT: B 165 HIS cc_start: 0.8345 (t-90) cc_final: 0.7923 (t70) REVERT: B 232 ILE cc_start: 0.9646 (pt) cc_final: 0.9262 (mt) REVERT: C 81 ASP cc_start: 0.8678 (t0) cc_final: 0.8452 (t0) REVERT: D 34 GLU cc_start: 0.9381 (mp0) cc_final: 0.9071 (pm20) REVERT: D 42 LYS cc_start: 0.9262 (mmtt) cc_final: 0.8813 (mmmm) REVERT: D 178 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8402 (mm-30) REVERT: E 36 ASN cc_start: 0.9565 (m110) cc_final: 0.9179 (m-40) REVERT: E 50 MET cc_start: 0.9030 (mtp) cc_final: 0.8552 (mtp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.4406 time to fit residues: 92.1694 Evaluate side-chains 113 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11755 Z= 0.165 Angle : 0.542 6.560 15976 Z= 0.293 Chirality : 0.042 0.154 1750 Planarity : 0.004 0.060 2102 Dihedral : 5.471 31.755 1615 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.65 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.39 (0.21), residues: 1461 helix: 0.70 (0.30), residues: 303 sheet: -1.51 (0.23), residues: 405 loop : -2.69 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 48 HIS 0.005 0.001 HIS B 347 PHE 0.023 0.001 PHE A 648 TYR 0.013 0.001 TYR A 504 ARG 0.004 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.820 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 ASP cc_start: 0.8728 (t0) cc_final: 0.8435 (m-30) REVERT: B 165 HIS cc_start: 0.8271 (t-90) cc_final: 0.7858 (t70) REVERT: B 232 ILE cc_start: 0.9661 (pt) cc_final: 0.9274 (mt) REVERT: C 81 ASP cc_start: 0.8710 (t0) cc_final: 0.8483 (t0) REVERT: D 34 GLU cc_start: 0.9372 (mp0) cc_final: 0.9066 (pm20) REVERT: D 42 LYS cc_start: 0.9273 (mmtt) cc_final: 0.8828 (mmmm) REVERT: D 178 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8429 (mm-30) REVERT: E 36 ASN cc_start: 0.9557 (m110) cc_final: 0.9125 (m-40) REVERT: E 50 MET cc_start: 0.9007 (mtp) cc_final: 0.8532 (mtp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4199 time to fit residues: 82.8795 Evaluate side-chains 112 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11755 Z= 0.254 Angle : 0.580 4.893 15976 Z= 0.321 Chirality : 0.042 0.151 1750 Planarity : 0.004 0.060 2102 Dihedral : 5.576 35.093 1615 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.58 (0.21), residues: 1461 helix: 0.43 (0.30), residues: 301 sheet: -1.64 (0.23), residues: 440 loop : -2.75 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 376 HIS 0.006 0.002 HIS B 165 PHE 0.018 0.001 PHE D 95 TYR 0.015 0.002 TYR A 416 ARG 0.005 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.845 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: 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 503 ASP cc_start: 0.8774 (t0) cc_final: 0.8450 (m-30) REVERT: A 545 MET cc_start: 0.9529 (mmp) cc_final: 0.8723 (mmp) REVERT: A 630 LEU cc_start: 0.9517 (tp) cc_final: 0.9216 (tp) REVERT: B 232 ILE cc_start: 0.9674 (pt) cc_final: 0.9308 (mt) REVERT: C 81 ASP cc_start: 0.8747 (t0) cc_final: 0.8496 (t0) REVERT: D 34 GLU cc_start: 0.9372 (mp0) cc_final: 0.9066 (pm20) REVERT: D 42 LYS cc_start: 0.9335 (mmtt) cc_final: 0.8912 (mmmm) REVERT: D 178 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8544 (mm-30) REVERT: E 36 ASN cc_start: 0.9426 (m110) cc_final: 0.9047 (m-40) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.4026 time to fit residues: 80.5636 Evaluate side-chains 106 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 132 optimal weight: 0.0970 chunk 115 optimal weight: 0.0770 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 542 GLN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11755 Z= 0.139 Angle : 0.531 5.586 15976 Z= 0.285 Chirality : 0.043 0.155 1750 Planarity : 0.004 0.058 2102 Dihedral : 5.278 32.060 1615 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.28 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.18 (0.22), residues: 1461 helix: 0.88 (0.30), residues: 301 sheet: -1.39 (0.24), residues: 414 loop : -2.54 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 376 HIS 0.007 0.001 HIS B 347 PHE 0.012 0.001 PHE D 95 TYR 0.012 0.001 TYR A 504 ARG 0.004 0.000 ARG B 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.878 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: 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: symmetry clash revert: symmetry clash REVERT: A 748 ASN cc_start: 0.8101 (m-40) cc_final: 0.7773 (m110) REVERT: B 232 ILE cc_start: 0.9671 (pt) cc_final: 0.9280 (mt) REVERT: C 81 ASP cc_start: 0.8754 (t0) cc_final: 0.8524 (t0) REVERT: D 34 GLU cc_start: 0.9355 (mp0) cc_final: 0.9034 (pm20) REVERT: D 42 LYS cc_start: 0.9268 (mmtt) cc_final: 0.8825 (mmmm) REVERT: D 178 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8407 (mm-30) REVERT: E 36 ASN cc_start: 0.9547 (m110) cc_final: 0.9154 (m-40) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3999 time to fit residues: 81.3351 Evaluate side-chains 108 residues out of total 1234 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.044274 restraints weight = 173551.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.046941 restraints weight = 81755.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.048789 restraints weight = 48188.931| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 11755 Z= 0.397 Angle : 0.665 5.790 15976 Z= 0.372 Chirality : 0.042 0.153 1750 Planarity : 0.005 0.065 2102 Dihedral : 5.655 36.360 1615 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.00 % Favored : 86.93 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.80 (0.21), residues: 1461 helix: -0.06 (0.28), residues: 303 sheet: -1.59 (0.23), residues: 427 loop : -2.87 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 376 HIS 0.010 0.002 HIS B 165 PHE 0.023 0.002 PHE D 95 TYR 0.020 0.002 TYR A 416 ARG 0.007 0.000 ARG B 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4187.32 seconds wall clock time: 74 minutes 4.24 seconds (4444.24 seconds total)