Starting phenix.real_space_refine on Sat Dec 9 16:06:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/12_2023/7qe5_13930_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/12_2023/7qe5_13930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/12_2023/7qe5_13930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/12_2023/7qe5_13930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/12_2023/7qe5_13930_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/12_2023/7qe5_13930_neut.pdb" } resolution = 4.7 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= 0.024 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 37 5.16 5 C 3793 2.51 5 N 905 2.21 5 O 985 1.98 5 H 5932 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 181": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 317": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 386": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 390": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 573": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 476": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 510": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 536": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 549": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11652 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9794 Classifications: {'peptide': 616} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 588} Chain: "B" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1858 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain breaks: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.49 Number of scatterers: 11652 At special positions: 0 Unit cell: (108.36, 94.6, 86, 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 37 16.00 O 985 8.00 N 905 7.00 C 3793 6.00 H 5932 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 534 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 74.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.527A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 removed outlier: 3.661A pdb=" N GLU A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.873A pdb=" N ASN A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 107 removed outlier: 3.884A pdb=" N PHE A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 121 through 149 removed outlier: 4.355A pdb=" N PHE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 155 through 173 removed outlier: 4.073A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 180 through 186 removed outlier: 6.301A pdb=" N SER A 183 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 186 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.720A pdb=" N PHE A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.879A pdb=" N THR A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 262 removed outlier: 4.109A pdb=" N ALA A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 263 through 276 removed outlier: 4.280A pdb=" N ARG A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 299 removed outlier: 4.137A pdb=" N LEU A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 removed outlier: 5.585A pdb=" N GLN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 340 removed outlier: 3.504A pdb=" N GLY A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 387 removed outlier: 3.501A pdb=" N LEU A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 4.247A pdb=" N LYS A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 422 removed outlier: 4.229A pdb=" N TRP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix removed outlier: 3.574A pdb=" N ILE A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 445 Processing helix chain 'A' and resid 452 through 486 removed outlier: 3.537A pdb=" N GLU A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.738A pdb=" N ARG A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 removed outlier: 3.504A pdb=" N VAL A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 5.206A pdb=" N PHE A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Proline residue: A 531 - end of helix Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.504A pdb=" N VAL A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 576 removed outlier: 3.783A pdb=" N PHE A 569 " --> pdb=" O GLY A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.652A pdb=" N LYS A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 603 removed outlier: 3.578A pdb=" N VAL A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.141A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'B' and resid 525 through 529 Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.708A pdb=" N LEU B 456 " --> pdb=" O MET B 521 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 473 through 477 removed outlier: 4.384A pdb=" N ALA B 530 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 559 " --> pdb=" O ALA B 530 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 9.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 5927 1.13 - 1.30: 903 1.30 - 1.48: 2290 1.48 - 1.65: 2601 1.65 - 1.83: 67 Bond restraints: 11788 Sorted by residual: bond pdb=" N ARG B 483 " pdb=" H ARG B 483 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" N SER B 543 " pdb=" H SER B 543 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N ARG A 80 " pdb=" H ARG A 80 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N TYR B 552 " pdb=" H TYR B 552 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N TRP B 553 " pdb=" H TRP B 553 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 ... (remaining 11783 not shown) Histogram of bond angle deviations from ideal: 87.41 - 96.97: 3 96.97 - 106.54: 738 106.54 - 116.10: 13833 116.10 - 125.67: 6627 125.67 - 135.23: 175 Bond angle restraints: 21376 Sorted by residual: angle pdb=" C TYR B 550 " pdb=" CA TYR B 550 " pdb=" CB TYR B 550 " ideal model delta sigma weight residual 110.68 87.41 23.27 1.70e+00 3.46e-01 1.87e+02 angle pdb=" CA ASP B 471 " pdb=" CB ASP B 471 " pdb=" CG ASP B 471 " ideal model delta sigma weight residual 112.60 122.37 -9.77 1.00e+00 1.00e+00 9.55e+01 angle pdb=" C PRO A 76 " pdb=" CA PRO A 76 " pdb=" CB PRO A 76 " ideal model delta sigma weight residual 111.22 97.57 13.65 1.51e+00 4.39e-01 8.17e+01 angle pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " pdb=" CG PHE A 222 " ideal model delta sigma weight residual 113.80 122.71 -8.91 1.00e+00 1.00e+00 7.94e+01 angle pdb=" N TYR B 552 " pdb=" CA TYR B 552 " pdb=" C TYR B 552 " ideal model delta sigma weight residual 108.14 121.26 -13.12 1.52e+00 4.33e-01 7.45e+01 ... (remaining 21371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4873 17.40 - 34.79: 368 34.79 - 52.19: 68 52.19 - 69.58: 82 69.58 - 86.98: 11 Dihedral angle restraints: 5402 sinusoidal: 2816 harmonic: 2586 Sorted by residual: dihedral pdb=" C TYR B 550 " pdb=" N TYR B 550 " pdb=" CA TYR B 550 " pdb=" CB TYR B 550 " ideal model delta harmonic sigma weight residual -122.60 -103.61 -18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C ILE A 615 " pdb=" N ILE A 615 " pdb=" CA ILE A 615 " pdb=" CB ILE A 615 " ideal model delta harmonic sigma weight residual -122.00 -139.87 17.87 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" CD ARG B 536 " pdb=" NE ARG B 536 " pdb=" CZ ARG B 536 " pdb=" NH1 ARG B 536 " ideal model delta sinusoidal sigma weight residual 0.00 57.93 -57.93 1 1.00e+01 1.00e-02 4.50e+01 ... (remaining 5399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 706 0.112 - 0.224: 195 0.224 - 0.336: 33 0.336 - 0.448: 7 0.448 - 0.560: 2 Chirality restraints: 943 Sorted by residual: chirality pdb=" CA ILE A 615 " pdb=" N ILE A 615 " pdb=" C ILE A 615 " pdb=" CB ILE A 615 " both_signs ideal model delta sigma weight residual False 2.43 1.87 0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA GLN A 143 " pdb=" N GLN A 143 " pdb=" C GLN A 143 " pdb=" CB GLN A 143 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" CA HIS B 470 " pdb=" N HIS B 470 " pdb=" C HIS B 470 " pdb=" CB HIS B 470 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 940 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 536 " 1.338 9.50e-02 1.11e+02 4.59e-01 4.67e+02 pdb=" NE ARG B 536 " 0.132 2.00e-02 2.50e+03 pdb=" CZ ARG B 536 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 536 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG B 536 " -0.068 2.00e-02 2.50e+03 pdb="HH11 ARG B 536 " -0.187 2.00e-02 2.50e+03 pdb="HH12 ARG B 536 " 0.149 2.00e-02 2.50e+03 pdb="HH21 ARG B 536 " -0.128 2.00e-02 2.50e+03 pdb="HH22 ARG B 536 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 546 " -0.124 2.00e-02 2.50e+03 1.36e-01 2.78e+02 pdb=" CG ASN B 546 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN B 546 " 0.143 2.00e-02 2.50e+03 pdb=" ND2 ASN B 546 " -0.076 2.00e-02 2.50e+03 pdb="HD21 ASN B 546 " 0.211 2.00e-02 2.50e+03 pdb="HD22 ASN B 546 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 477 " -0.128 2.00e-02 2.50e+03 1.23e-01 2.27e+02 pdb=" CD GLN B 477 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN B 477 " 0.103 2.00e-02 2.50e+03 pdb=" NE2 GLN B 477 " 0.083 2.00e-02 2.50e+03 pdb="HE21 GLN B 477 " 0.125 2.00e-02 2.50e+03 pdb="HE22 GLN B 477 " -0.203 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 725 2.19 - 2.79: 21236 2.79 - 3.39: 33116 3.39 - 4.00: 41706 4.00 - 4.60: 60408 Nonbonded interactions: 157191 Sorted by model distance: nonbonded pdb=" O THR A 330 " pdb=" HG SER A 333 " model vdw 1.586 1.850 nonbonded pdb=" HG SER A 426 " pdb=" OE2 GLU A 429 " model vdw 1.609 1.850 nonbonded pdb=" HH TYR A 221 " pdb=" OE2 GLU A 485 " model vdw 1.616 1.850 nonbonded pdb=" O LEU A 54 " pdb=" HG SER A 57 " model vdw 1.622 1.850 nonbonded pdb=" OD1 ASP B 468 " pdb=" HG SER B 491 " model vdw 1.632 1.850 ... (remaining 157186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.370 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: 0.160 Extract box with map and model: 2.060 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 40.280 Find NCS groups from input model: 0.180 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 : 0.013 0.092 5856 Z= 0.850 Angle : 2.056 23.272 7955 Z= 1.372 Chirality : 0.108 0.560 943 Planarity : 0.023 0.473 973 Dihedral : 14.367 86.978 2058 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.77 % Favored : 94.96 % Rotamer: Outliers : 1.14 % Allowed : 8.28 % Favored : 90.58 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.26), residues: 734 helix: -1.69 (0.18), residues: 471 sheet: -1.82 (1.41), residues: 15 loop : -1.37 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.023 TRP A 227 HIS 0.010 0.004 HIS A 65 PHE 0.107 0.015 PHE A 48 TYR 0.152 0.026 TYR A 252 ARG 0.022 0.002 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 214 time to evaluate : 0.894 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 218 average time/residue: 0.3418 time to fit residues: 99.5436 Evaluate side-chains 184 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 0.900 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.1711 time to fit residues: 1.9777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 285 HIS ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5856 Z= 0.282 Angle : 0.795 9.327 7955 Z= 0.453 Chirality : 0.043 0.175 943 Planarity : 0.009 0.144 973 Dihedral : 7.847 30.798 787 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 0.16 % Allowed : 3.73 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.67 (0.29), residues: 734 helix: -0.72 (0.21), residues: 467 sheet: -1.72 (0.81), residues: 40 loop : -1.49 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 553 HIS 0.007 0.002 HIS A 65 PHE 0.027 0.002 PHE A 361 TYR 0.033 0.003 TYR B 550 ARG 0.003 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.866 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.3152 time to fit residues: 83.6065 Evaluate side-chains 173 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2273 time to fit residues: 1.3961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.0770 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5856 Z= 0.220 Angle : 0.699 9.755 7955 Z= 0.388 Chirality : 0.041 0.168 943 Planarity : 0.007 0.089 973 Dihedral : 7.036 29.399 787 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 0.16 % Allowed : 1.95 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.29), residues: 734 helix: -0.10 (0.22), residues: 458 sheet: -1.12 (1.14), residues: 25 loop : -1.56 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 474 HIS 0.020 0.003 HIS A 285 PHE 0.021 0.002 PHE A 98 TYR 0.022 0.002 TYR B 550 ARG 0.006 0.001 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.935 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.3388 time to fit residues: 88.2536 Evaluate side-chains 171 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2354 time to fit residues: 1.4512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5856 Z= 0.200 Angle : 0.621 8.677 7955 Z= 0.348 Chirality : 0.040 0.169 943 Planarity : 0.006 0.084 973 Dihedral : 6.595 29.362 787 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.90 % Favored : 94.96 % Rotamer: Outliers : 0.16 % Allowed : 1.79 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 734 helix: 0.31 (0.23), residues: 465 sheet: -1.16 (0.85), residues: 43 loop : -1.28 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 544 HIS 0.008 0.002 HIS A 285 PHE 0.022 0.002 PHE A 98 TYR 0.014 0.002 TYR B 550 ARG 0.005 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.970 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 201 average time/residue: 0.3073 time to fit residues: 84.7741 Evaluate side-chains 181 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2055 time to fit residues: 1.4972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5856 Z= 0.400 Angle : 0.795 9.461 7955 Z= 0.460 Chirality : 0.044 0.226 943 Planarity : 0.007 0.085 973 Dihedral : 7.011 32.504 787 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.63 % Favored : 92.23 % Rotamer: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -1.49 (0.29), residues: 734 helix: -0.44 (0.22), residues: 472 sheet: -1.54 (0.82), residues: 45 loop : -1.82 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 408 HIS 0.007 0.003 HIS A 34 PHE 0.026 0.003 PHE A 222 TYR 0.031 0.003 TYR A 349 ARG 0.007 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.050 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: symmetry clash outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.3605 time to fit residues: 98.1376 Evaluate side-chains 178 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2289 time to fit residues: 1.9048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5856 Z= 0.253 Angle : 0.674 7.480 7955 Z= 0.380 Chirality : 0.040 0.178 943 Planarity : 0.006 0.081 973 Dihedral : 6.701 33.611 787 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.99 (0.30), residues: 734 helix: -0.05 (0.23), residues: 468 sheet: -0.97 (0.88), residues: 37 loop : -1.69 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 553 HIS 0.004 0.002 HIS A 34 PHE 0.046 0.002 PHE A 361 TYR 0.027 0.002 TYR B 540 ARG 0.003 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.801 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 outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2719 time to fit residues: 75.6991 Evaluate side-chains 181 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.6607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5856 Z= 0.198 Angle : 0.634 8.666 7955 Z= 0.348 Chirality : 0.040 0.181 943 Planarity : 0.006 0.099 973 Dihedral : 6.329 35.199 787 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.42 (0.31), residues: 734 helix: 0.35 (0.24), residues: 467 sheet: -0.74 (0.89), residues: 37 loop : -1.33 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 544 HIS 0.004 0.002 HIS A 100 PHE 0.024 0.002 PHE A 361 TYR 0.023 0.002 TYR B 550 ARG 0.004 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.716 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 outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2904 time to fit residues: 80.9392 Evaluate side-chains 175 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5856 Z= 0.203 Angle : 0.632 9.841 7955 Z= 0.347 Chirality : 0.040 0.177 943 Planarity : 0.005 0.073 973 Dihedral : 6.209 31.164 787 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.27 (0.31), residues: 734 helix: 0.46 (0.24), residues: 467 sheet: -0.83 (0.90), residues: 37 loop : -1.26 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.004 0.001 HIS A 100 PHE 0.020 0.002 PHE A 361 TYR 0.025 0.002 TYR B 550 ARG 0.003 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.877 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 outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2892 time to fit residues: 78.4825 Evaluate side-chains 172 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5856 Z= 0.198 Angle : 0.612 7.766 7955 Z= 0.335 Chirality : 0.039 0.164 943 Planarity : 0.005 0.069 973 Dihedral : 5.973 29.346 787 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.31), residues: 734 helix: 0.57 (0.24), residues: 469 sheet: -1.22 (0.88), residues: 37 loop : -1.24 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 474 HIS 0.004 0.001 HIS A 285 PHE 0.019 0.001 PHE A 361 TYR 0.024 0.002 TYR B 550 ARG 0.004 0.000 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.920 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.3051 time to fit residues: 82.3473 Evaluate side-chains 177 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.899 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5856 Z= 0.188 Angle : 0.596 6.844 7955 Z= 0.324 Chirality : 0.039 0.164 943 Planarity : 0.005 0.067 973 Dihedral : 5.823 28.194 787 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 734 helix: 0.69 (0.24), residues: 469 sheet: -1.37 (0.87), residues: 37 loop : -1.22 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.004 0.001 HIS A 100 PHE 0.014 0.001 PHE A 361 TYR 0.022 0.002 TYR B 550 ARG 0.006 0.000 ARG B 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1468 Ramachandran restraints generated. 734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.974 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 outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3104 time to fit residues: 82.4313 Evaluate side-chains 171 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 59 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 41 optimal weight: 0.3980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.089708 restraints weight = 62768.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093803 restraints weight = 33556.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096706 restraints weight = 20531.530| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5856 Z= 0.165 Angle : 0.579 6.806 7955 Z= 0.309 Chirality : 0.039 0.159 943 Planarity : 0.005 0.059 973 Dihedral : 5.545 27.988 787 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.32), residues: 734 helix: 0.81 (0.24), residues: 472 sheet: -1.17 (0.89), residues: 37 loop : -1.02 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 474 HIS 0.004 0.001 HIS A 100 PHE 0.014 0.001 PHE A 139 TYR 0.017 0.002 TYR B 550 ARG 0.006 0.000 ARG B 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.32 seconds wall clock time: 60 minutes 37.94 seconds (3637.94 seconds total)