Starting phenix.real_space_refine on Fri Mar 15 12:09:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/03_2024/7qe5_13930_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/03_2024/7qe5_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_13930/03_2024/7qe5_13930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/03_2024/7qe5_13930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/03_2024/7qe5_13930_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qe5_13930/03_2024/7qe5_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-dev-5265/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: 5.47, per 1000 atoms: 0.47 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: 9.07 Conformation dependent library (CDL) restraints added in 1.2 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: 0.80 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: 3.92 Time building geometry restraints manager: 9.50 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: 4908 17.40 - 34.79: 394 34.79 - 52.19: 113 52.19 - 69.58: 116 69.58 - 86.98: 11 Dihedral angle restraints: 5542 sinusoidal: 2956 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 5539 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: 0.400 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: 0.180 Extract box with map and model: 2.170 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 39.960 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- 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 : 0.939 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: A 1 MET cc_start: 0.8233 (tpt) cc_final: 0.8028 (tpp) REVERT: A 27 ILE cc_start: 0.9196 (tp) cc_final: 0.8806 (tp) REVERT: A 63 GLN cc_start: 0.8598 (tp40) cc_final: 0.7780 (mt0) REVERT: A 78 LYS cc_start: 0.2644 (OUTLIER) cc_final: 0.2330 (tmtt) REVERT: A 97 LEU cc_start: 0.8563 (mm) cc_final: 0.8361 (mm) REVERT: A 158 PHE cc_start: 0.7614 (t80) cc_final: 0.7239 (t80) REVERT: A 283 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7491 (mmt) REVERT: A 317 ARG cc_start: 0.9302 (ttt180) cc_final: 0.8817 (ttp80) REVERT: A 339 LEU cc_start: 0.8425 (mt) cc_final: 0.8176 (mt) REVERT: A 518 MET cc_start: 0.8796 (mtm) cc_final: 0.8452 (mtm) REVERT: A 556 MET cc_start: 0.8388 (mtp) cc_final: 0.8029 (mtp) REVERT: A 589 PHE cc_start: 0.8610 (m-80) cc_final: 0.8239 (m-80) outliers start: 7 outliers final: 3 residues processed: 218 average time/residue: 0.3385 time to fit residues: 99.1380 Evaluate side-chains 188 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.7980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 66 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 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: 0.7043 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5856 Z= 0.284 Angle : 0.802 9.635 7955 Z= 0.455 Chirality : 0.044 0.176 943 Planarity : 0.009 0.140 973 Dihedral : 7.782 30.921 787 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.27 % 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: -1.64 (0.28), residues: 734 helix: -0.71 (0.21), residues: 467 sheet: -1.68 (0.82), residues: 40 loop : -1.47 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 553 HIS 0.007 0.002 HIS A 65 PHE 0.026 0.002 PHE A 361 TYR 0.034 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 : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 27 ILE cc_start: 0.9064 (tp) cc_final: 0.8572 (tp) REVERT: A 63 GLN cc_start: 0.8400 (tp40) cc_final: 0.8162 (tp40) REVERT: A 158 PHE cc_start: 0.7519 (t80) cc_final: 0.7194 (t80) REVERT: A 235 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 330 THR cc_start: 0.8961 (t) cc_final: 0.8717 (t) REVERT: A 405 GLN cc_start: 0.8847 (pt0) cc_final: 0.7855 (tm-30) REVERT: A 412 THR cc_start: 0.9208 (m) cc_final: 0.8991 (m) REVERT: A 518 MET cc_start: 0.8793 (mtm) cc_final: 0.8470 (mtm) REVERT: A 527 PHE cc_start: 0.7982 (m-80) cc_final: 0.7341 (m-80) REVERT: A 532 MET cc_start: 0.9026 (pmm) cc_final: 0.7835 (pmm) REVERT: A 533 LEU cc_start: 0.8684 (mt) cc_final: 0.8116 (mt) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.3058 time to fit residues: 81.8005 Evaluate side-chains 177 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 558 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5856 Z= 0.225 Angle : 0.690 8.880 7955 Z= 0.387 Chirality : 0.041 0.160 943 Planarity : 0.007 0.100 973 Dihedral : 7.015 29.238 787 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -1.04 (0.29), residues: 734 helix: -0.13 (0.22), residues: 459 sheet: -1.19 (0.88), residues: 41 loop : -1.52 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 544 HIS 0.018 0.003 HIS A 285 PHE 0.022 0.002 PHE A 98 TYR 0.020 0.002 TYR B 550 ARG 0.006 0.001 ARG A 80 *********************** 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 194 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.893 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: A 63 GLN cc_start: 0.8294 (tp40) cc_final: 0.7990 (tp40) REVERT: A 158 PHE cc_start: 0.7643 (t80) cc_final: 0.7396 (t80) REVERT: A 235 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 258 LEU cc_start: 0.9124 (mt) cc_final: 0.8892 (mt) REVERT: A 259 MET cc_start: 0.8628 (tpp) cc_final: 0.8415 (tpp) REVERT: A 283 MET cc_start: 0.7410 (mmt) cc_final: 0.6993 (mmt) REVERT: A 330 THR cc_start: 0.8823 (t) cc_final: 0.8523 (t) REVERT: A 405 GLN cc_start: 0.8706 (pt0) cc_final: 0.8046 (tm-30) REVERT: A 518 MET cc_start: 0.8699 (mtm) cc_final: 0.8380 (mtm) REVERT: A 532 MET cc_start: 0.8896 (pmm) cc_final: 0.7727 (pmm) REVERT: A 533 LEU cc_start: 0.8704 (mt) cc_final: 0.8042 (mt) REVERT: A 544 LEU cc_start: 0.8277 (mt) cc_final: 0.7928 (mt) REVERT: A 589 PHE cc_start: 0.9039 (m-10) cc_final: 0.8803 (m-10) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3170 time to fit residues: 83.2876 Evaluate side-chains 172 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5856 Z= 0.210 Angle : 0.633 9.819 7955 Z= 0.353 Chirality : 0.040 0.179 943 Planarity : 0.006 0.084 973 Dihedral : 6.561 30.408 787 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.69 (0.30), residues: 734 helix: 0.18 (0.23), residues: 465 sheet: -1.29 (0.88), residues: 41 loop : -1.43 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 408 HIS 0.003 0.001 HIS A 34 PHE 0.020 0.002 PHE A 98 TYR 0.027 0.002 TYR A 349 ARG 0.004 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 197 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.840 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: A 63 GLN cc_start: 0.8336 (tp40) cc_final: 0.8124 (tp40) REVERT: A 158 PHE cc_start: 0.7683 (t80) cc_final: 0.7394 (t80) REVERT: A 258 LEU cc_start: 0.9149 (mt) cc_final: 0.8913 (mt) REVERT: A 259 MET cc_start: 0.8462 (tpp) cc_final: 0.8123 (tpp) REVERT: A 283 MET cc_start: 0.7145 (mmt) cc_final: 0.6696 (mmt) REVERT: A 316 MET cc_start: 0.8747 (mmm) cc_final: 0.8501 (mmm) REVERT: A 317 ARG cc_start: 0.9479 (ttt180) cc_final: 0.9056 (ttp-170) REVERT: A 330 THR cc_start: 0.8868 (t) cc_final: 0.8520 (t) REVERT: A 338 PRO cc_start: 0.8832 (Cg_exo) cc_final: 0.8600 (Cg_endo) REVERT: A 405 GLN cc_start: 0.8821 (pt0) cc_final: 0.7874 (tm-30) REVERT: A 412 THR cc_start: 0.8999 (m) cc_final: 0.8728 (m) REVERT: A 447 LYS cc_start: 0.7331 (mmtt) cc_final: 0.6990 (mmtm) REVERT: A 518 MET cc_start: 0.8799 (mtm) cc_final: 0.8472 (mtm) REVERT: A 532 MET cc_start: 0.8926 (pmm) cc_final: 0.7548 (pmm) REVERT: A 533 LEU cc_start: 0.8724 (mt) cc_final: 0.7937 (mt) REVERT: A 544 LEU cc_start: 0.8436 (mt) cc_final: 0.8223 (mt) REVERT: A 589 PHE cc_start: 0.9097 (m-10) cc_final: 0.8847 (m-10) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3113 time to fit residues: 84.1469 Evaluate side-chains 178 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5856 Z= 0.233 Angle : 0.640 8.022 7955 Z= 0.361 Chirality : 0.040 0.161 943 Planarity : 0.006 0.081 973 Dihedral : 6.337 29.717 787 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.18 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -0.62 (0.31), residues: 734 helix: 0.23 (0.23), residues: 465 sheet: -1.55 (0.87), residues: 44 loop : -1.34 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 39 HIS 0.004 0.001 HIS A 34 PHE 0.014 0.002 PHE A 16 TYR 0.018 0.002 TYR B 533 ARG 0.009 0.001 ARG A 80 *********************** 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 193 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.883 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: A 125 PHE cc_start: 0.8443 (m-80) cc_final: 0.8149 (m-80) REVERT: A 158 PHE cc_start: 0.7714 (t80) cc_final: 0.7436 (t80) REVERT: A 254 LEU cc_start: 0.9420 (tp) cc_final: 0.9200 (tp) REVERT: A 259 MET cc_start: 0.8513 (tpp) cc_final: 0.8157 (tpp) REVERT: A 316 MET cc_start: 0.8872 (mmm) cc_final: 0.8512 (mmm) REVERT: A 317 ARG cc_start: 0.9473 (ttt180) cc_final: 0.9075 (ttp-170) REVERT: A 330 THR cc_start: 0.8957 (t) cc_final: 0.8607 (t) REVERT: A 405 GLN cc_start: 0.8914 (pt0) cc_final: 0.7922 (tm-30) REVERT: A 412 THR cc_start: 0.9135 (m) cc_final: 0.8907 (m) REVERT: A 518 MET cc_start: 0.8773 (mtm) cc_final: 0.8430 (mtm) REVERT: A 527 PHE cc_start: 0.8198 (m-80) cc_final: 0.7677 (m-80) REVERT: A 532 MET cc_start: 0.8921 (pmm) cc_final: 0.7178 (pmm) REVERT: A 533 LEU cc_start: 0.8702 (mt) cc_final: 0.7840 (mt) REVERT: A 589 PHE cc_start: 0.9068 (m-10) cc_final: 0.8831 (m-10) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2944 time to fit residues: 77.8195 Evaluate side-chains 181 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5856 Z= 0.184 Angle : 0.615 8.222 7955 Z= 0.337 Chirality : 0.039 0.172 943 Planarity : 0.005 0.078 973 Dihedral : 6.091 30.753 787 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % 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 : 0.14 % 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: -0.34 (0.31), residues: 734 helix: 0.46 (0.23), residues: 466 sheet: -1.36 (0.86), residues: 44 loop : -1.27 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 553 HIS 0.006 0.002 HIS A 100 PHE 0.012 0.001 PHE A 16 TYR 0.032 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 197 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.874 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 125 PHE cc_start: 0.8487 (m-80) cc_final: 0.8267 (m-80) REVERT: A 158 PHE cc_start: 0.7653 (t80) cc_final: 0.7372 (t80) REVERT: A 236 LYS cc_start: 0.8732 (ttmt) cc_final: 0.8148 (tppt) REVERT: A 254 LEU cc_start: 0.9426 (tp) cc_final: 0.9167 (tp) REVERT: A 259 MET cc_start: 0.8270 (tpp) cc_final: 0.7906 (tpp) REVERT: A 316 MET cc_start: 0.8845 (mmm) cc_final: 0.8559 (mmm) REVERT: A 317 ARG cc_start: 0.9451 (ttt180) cc_final: 0.9020 (ttp-170) REVERT: A 330 THR cc_start: 0.8940 (t) cc_final: 0.8570 (t) REVERT: A 412 THR cc_start: 0.9052 (m) cc_final: 0.8814 (m) REVERT: A 527 PHE cc_start: 0.8304 (m-80) cc_final: 0.7608 (m-80) REVERT: A 532 MET cc_start: 0.8886 (pmm) cc_final: 0.7455 (pmm) REVERT: A 544 LEU cc_start: 0.8639 (mt) cc_final: 0.8388 (mt) REVERT: A 589 PHE cc_start: 0.8986 (m-10) cc_final: 0.8712 (m-10) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2994 time to fit residues: 81.0820 Evaluate side-chains 184 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5856 Z= 0.194 Angle : 0.606 7.411 7955 Z= 0.333 Chirality : 0.040 0.180 943 Planarity : 0.005 0.076 973 Dihedral : 5.917 32.030 787 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: -0.16 (0.31), residues: 734 helix: 0.60 (0.23), residues: 465 sheet: -1.35 (0.87), residues: 44 loop : -1.19 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 553 HIS 0.006 0.001 HIS A 100 PHE 0.021 0.001 PHE A 495 TYR 0.026 0.002 TYR A 349 ARG 0.003 0.000 ARG B 536 *********************** 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 198 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.844 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: A 125 PHE cc_start: 0.8399 (m-80) cc_final: 0.8180 (m-80) REVERT: A 158 PHE cc_start: 0.7682 (t80) cc_final: 0.7413 (t80) REVERT: A 236 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8177 (tppt) REVERT: A 237 LEU cc_start: 0.9392 (tp) cc_final: 0.9026 (tp) REVERT: A 254 LEU cc_start: 0.9434 (tp) cc_final: 0.9177 (tp) REVERT: A 259 MET cc_start: 0.8299 (tpp) cc_final: 0.7933 (tpp) REVERT: A 316 MET cc_start: 0.8859 (mmm) cc_final: 0.8584 (mmm) REVERT: A 317 ARG cc_start: 0.9449 (ttt180) cc_final: 0.9020 (ttp-170) REVERT: A 330 THR cc_start: 0.8962 (t) cc_final: 0.8609 (t) REVERT: A 405 GLN cc_start: 0.8829 (pt0) cc_final: 0.7908 (tm-30) REVERT: A 412 THR cc_start: 0.9067 (m) cc_final: 0.8835 (m) REVERT: A 527 PHE cc_start: 0.8351 (m-80) cc_final: 0.7697 (m-80) REVERT: A 529 VAL cc_start: 0.9386 (m) cc_final: 0.9139 (m) REVERT: A 532 MET cc_start: 0.8933 (pmm) cc_final: 0.7159 (pmm) REVERT: A 533 LEU cc_start: 0.8664 (mt) cc_final: 0.7752 (mt) REVERT: A 544 LEU cc_start: 0.8715 (mt) cc_final: 0.8514 (mt) REVERT: A 556 MET cc_start: 0.7880 (mtp) cc_final: 0.7605 (mtp) REVERT: A 564 MET cc_start: 0.7142 (tpt) cc_final: 0.6937 (tpp) REVERT: A 589 PHE cc_start: 0.8997 (m-10) cc_final: 0.8717 (m-10) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2918 time to fit residues: 79.9998 Evaluate side-chains 180 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7159 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5856 Z= 0.195 Angle : 0.599 7.206 7955 Z= 0.332 Chirality : 0.040 0.177 943 Planarity : 0.005 0.078 973 Dihedral : 5.817 29.764 787 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % 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 : 0.00 % 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: -0.05 (0.31), residues: 734 helix: 0.72 (0.24), residues: 463 sheet: -1.36 (0.86), residues: 44 loop : -1.19 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 39 HIS 0.005 0.001 HIS A 100 PHE 0.049 0.002 PHE A 361 TYR 0.022 0.002 TYR B 550 ARG 0.004 0.000 ARG B 549 *********************** 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 194 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.436 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 158 PHE cc_start: 0.7735 (t80) cc_final: 0.7429 (t80) REVERT: A 200 TRP cc_start: 0.9259 (t60) cc_final: 0.8802 (t60) REVERT: A 236 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8154 (tppt) REVERT: A 254 LEU cc_start: 0.9437 (tp) cc_final: 0.9180 (tp) REVERT: A 259 MET cc_start: 0.8317 (tpp) cc_final: 0.7983 (tpp) REVERT: A 316 MET cc_start: 0.8885 (mmm) cc_final: 0.8630 (mmm) REVERT: A 317 ARG cc_start: 0.9447 (ttt180) cc_final: 0.9046 (ttp-170) REVERT: A 330 THR cc_start: 0.8979 (t) cc_final: 0.8620 (t) REVERT: A 405 GLN cc_start: 0.8862 (pt0) cc_final: 0.7995 (tm-30) REVERT: A 527 PHE cc_start: 0.8392 (m-80) cc_final: 0.7641 (m-80) REVERT: A 532 MET cc_start: 0.8899 (pmm) cc_final: 0.7123 (pmm) REVERT: A 533 LEU cc_start: 0.8639 (mt) cc_final: 0.7737 (mt) REVERT: A 556 MET cc_start: 0.7881 (mtp) cc_final: 0.7632 (mtp) REVERT: A 564 MET cc_start: 0.7095 (tpt) cc_final: 0.6871 (tpp) REVERT: A 589 PHE cc_start: 0.9038 (m-10) cc_final: 0.8695 (m-10) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3285 time to fit residues: 87.8431 Evaluate side-chains 185 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 59 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7115 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5856 Z= 0.168 Angle : 0.573 6.756 7955 Z= 0.312 Chirality : 0.039 0.163 943 Planarity : 0.005 0.081 973 Dihedral : 5.579 33.034 787 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % 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 : 0.14 % 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: 0.24 (0.32), residues: 734 helix: 0.90 (0.24), residues: 467 sheet: -1.37 (0.85), residues: 44 loop : -0.97 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 553 HIS 0.007 0.001 HIS A 100 PHE 0.013 0.001 PHE A 495 TYR 0.018 0.002 TYR B 550 ARG 0.008 0.001 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 200 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.919 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 158 PHE cc_start: 0.7668 (t80) cc_final: 0.7371 (t80) REVERT: A 200 TRP cc_start: 0.9091 (t60) cc_final: 0.8647 (t60) REVERT: A 236 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8221 (tppt) REVERT: A 237 LEU cc_start: 0.9250 (tp) cc_final: 0.9039 (tp) REVERT: A 254 LEU cc_start: 0.9425 (tp) cc_final: 0.9171 (tp) REVERT: A 259 MET cc_start: 0.8263 (tpp) cc_final: 0.7928 (tpp) REVERT: A 316 MET cc_start: 0.8811 (mmm) cc_final: 0.8585 (mmm) REVERT: A 317 ARG cc_start: 0.9426 (ttt180) cc_final: 0.9044 (ttp-170) REVERT: A 330 THR cc_start: 0.8968 (t) cc_final: 0.8592 (t) REVERT: A 405 GLN cc_start: 0.8866 (pt0) cc_final: 0.7968 (tm-30) REVERT: A 532 MET cc_start: 0.8902 (pmm) cc_final: 0.7424 (pmm) REVERT: A 556 MET cc_start: 0.7872 (mtp) cc_final: 0.7658 (mtp) REVERT: A 589 PHE cc_start: 0.8999 (m-10) cc_final: 0.8663 (m-10) REVERT: A 594 PHE cc_start: 0.8622 (t80) cc_final: 0.8349 (t80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3053 time to fit residues: 84.1021 Evaluate side-chains 180 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 2.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** 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: 0.7174 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5856 Z= 0.185 Angle : 0.567 6.400 7955 Z= 0.314 Chirality : 0.039 0.161 943 Planarity : 0.005 0.080 973 Dihedral : 5.517 31.812 787 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % 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 : 0.14 % 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: 0.23 (0.32), residues: 734 helix: 0.91 (0.24), residues: 473 sheet: -1.39 (0.85), residues: 44 loop : -1.07 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 227 HIS 0.005 0.001 HIS A 100 PHE 0.015 0.001 PHE A 20 TYR 0.016 0.002 TYR B 550 ARG 0.009 0.001 ARG A 226 ********************** 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 194 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.041 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: A 158 PHE cc_start: 0.7755 (t80) cc_final: 0.7435 (t80) REVERT: A 164 VAL cc_start: 0.6101 (t) cc_final: 0.5884 (t) REVERT: A 200 TRP cc_start: 0.9145 (t60) cc_final: 0.8664 (t60) REVERT: A 236 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8224 (tppt) REVERT: A 254 LEU cc_start: 0.9448 (tp) cc_final: 0.9170 (tp) REVERT: A 259 MET cc_start: 0.8318 (tpp) cc_final: 0.7857 (tpp) REVERT: A 316 MET cc_start: 0.8818 (mmm) cc_final: 0.8550 (mmm) REVERT: A 317 ARG cc_start: 0.9408 (ttt180) cc_final: 0.9026 (ttp-170) REVERT: A 330 THR cc_start: 0.8993 (t) cc_final: 0.8614 (t) REVERT: A 405 GLN cc_start: 0.8911 (pt0) cc_final: 0.8008 (tm-30) REVERT: A 532 MET cc_start: 0.8946 (pmm) cc_final: 0.7441 (pmm) REVERT: A 556 MET cc_start: 0.8031 (mtp) cc_final: 0.7724 (mtp) REVERT: A 589 PHE cc_start: 0.9026 (m-10) cc_final: 0.8671 (m-10) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.3044 time to fit residues: 81.2886 Evaluate side-chains 172 residues out of total 616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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: 0.0970 chunk 8 optimal weight: 0.0770 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 overall best weight: 0.2112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 ASN ** 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 = 0.3646 r_free = 0.3646 target = 0.106186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.091209 restraints weight = 61754.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095453 restraints weight = 32512.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098438 restraints weight = 19581.767| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5856 Z= 0.162 Angle : 0.556 6.092 7955 Z= 0.301 Chirality : 0.039 0.159 943 Planarity : 0.005 0.080 973 Dihedral : 5.344 30.796 787 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.37 % 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 : 0.14 % 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: 0.60 (0.33), residues: 734 helix: 1.16 (0.24), residues: 469 sheet: -1.29 (0.84), residues: 44 loop : -0.77 (0.46), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.006 0.001 HIS A 100 PHE 0.028 0.001 PHE A 361 TYR 0.026 0.002 TYR B 533 ARG 0.008 0.000 ARG B 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3358.16 seconds wall clock time: 59 minutes 28.85 seconds (3568.85 seconds total)