Starting phenix.real_space_refine on Wed Feb 14 23:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8a_24313/02_2024/7r8a_24313_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8a_24313/02_2024/7r8a_24313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8a_24313/02_2024/7r8a_24313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8a_24313/02_2024/7r8a_24313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8a_24313/02_2024/7r8a_24313_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r8a_24313/02_2024/7r8a_24313_updated.pdb" } resolution = 2.9 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6810 2.51 5 N 1778 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 71": "OD1" <-> "OD2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 466": "OD1" <-> "OD2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 108": "NH1" <-> "NH2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 101": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10530 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4596 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 22, 'TRANS': 561} Chain breaks: 3 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4202 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.13, per 1000 atoms: 0.58 Number of scatterers: 10530 At special positions: 0 Unit cell: (117.316, 99.592, 128.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1876 8.00 N 1778 7.00 C 6810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 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: 4.38 Conformation dependent library (CDL) restraints added in 1.9 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 8 sheets defined 45.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 195 through 209 removed outlier: 4.550A pdb=" N GLN A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 333 through 346 Processing helix chain 'A' and resid 364 through 380 Processing helix chain 'A' and resid 383 through 403 removed outlier: 5.292A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 452 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 460 through 490 Proline residue: A 473 - end of helix removed outlier: 4.839A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 523 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 527 through 544 Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.608A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 620 through 647 removed outlier: 3.877A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 3.775A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 141 through 147 Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 245 through 259 Processing helix chain 'B' and resid 300 through 307 removed outlier: 3.534A pdb=" N ALA B 306 " --> pdb=" O GLN B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 445 through 472 removed outlier: 4.644A pdb=" N ILE B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 491 through 516 Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 586 through 593 Processing helix chain 'B' and resid 595 through 608 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 640 through 664 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing sheet with id= A, first strand: chain 'A' and resid 74 through 77 removed outlier: 4.477A pdb=" N VAL A 113 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 270 through 275 removed outlier: 6.676A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 245 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE A 84 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 247 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N GLY A 86 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 93 through 96 Processing sheet with id= D, first strand: chain 'B' and resid 290 through 296 removed outlier: 6.686A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 265 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE B 103 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 267 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N GLY B 105 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= F, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.048A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 24 through 27 Processing sheet with id= H, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.792A pdb=" N LYS D 123 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS D 59 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE D 64 " --> pdb=" O LYS D 59 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1509 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: 3.06 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3340 1.35 - 1.47: 2622 1.47 - 1.59: 4693 1.59 - 1.71: 0 1.71 - 1.83: 105 Bond restraints: 10760 Sorted by residual: bond pdb=" C10 CLR A 701 " pdb=" C5 CLR A 701 " ideal model delta sigma weight residual 1.519 1.450 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C10 CLR A 701 " pdb=" C19 CLR A 701 " ideal model delta sigma weight residual 1.536 1.485 0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" C1 CLR A 701 " pdb=" C10 CLR A 701 " ideal model delta sigma weight residual 1.544 1.498 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C13 CLR A 701 " pdb=" C18 CLR A 701 " ideal model delta sigma weight residual 1.532 1.486 0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C16 CLR A 701 " pdb=" C17 CLR A 701 " ideal model delta sigma weight residual 1.554 1.511 0.043 2.00e-02 2.50e+03 4.57e+00 ... (remaining 10755 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.79: 303 106.79 - 113.59: 5812 113.59 - 120.38: 4117 120.38 - 127.17: 4241 127.17 - 133.97: 96 Bond angle restraints: 14569 Sorted by residual: angle pdb=" N GLN A 310 " pdb=" CA GLN A 310 " pdb=" C GLN A 310 " ideal model delta sigma weight residual 114.56 108.87 5.69 1.27e+00 6.20e-01 2.01e+01 angle pdb=" C LEU B 458 " pdb=" N ILE B 459 " pdb=" CA ILE B 459 " ideal model delta sigma weight residual 120.24 122.77 -2.53 6.30e-01 2.52e+00 1.62e+01 angle pdb=" C ILE B 459 " pdb=" CA ILE B 459 " pdb=" CB ILE B 459 " ideal model delta sigma weight residual 114.35 110.19 4.16 1.06e+00 8.90e-01 1.54e+01 angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C16 CLR A 701 " pdb=" C17 CLR A 701 " pdb=" C20 CLR A 701 " ideal model delta sigma weight residual 112.02 101.92 10.10 3.00e+00 1.11e-01 1.13e+01 ... (remaining 14564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5846 17.52 - 35.04: 461 35.04 - 52.55: 112 52.55 - 70.07: 24 70.07 - 87.59: 7 Dihedral angle restraints: 6450 sinusoidal: 2606 harmonic: 3844 Sorted by residual: dihedral pdb=" CA THR A 358 " pdb=" C THR A 358 " pdb=" N LYS A 359 " pdb=" CA LYS A 359 " ideal model delta harmonic sigma weight residual 180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ILE C 114 " pdb=" C ILE C 114 " pdb=" N TYR C 115 " pdb=" CA TYR C 115 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU A 579 " pdb=" CG GLU A 579 " pdb=" CD GLU A 579 " pdb=" OE1 GLU A 579 " ideal model delta sinusoidal sigma weight residual 0.00 -87.59 87.59 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1583 0.089 - 0.178: 75 0.178 - 0.267: 2 0.267 - 0.356: 0 0.356 - 0.445: 2 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C10 CLR A 701 " pdb=" C1 CLR A 701 " pdb=" C5 CLR A 701 " pdb=" C9 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C17 CLR A 701 " pdb=" C13 CLR A 701 " pdb=" C16 CLR A 701 " pdb=" C20 CLR A 701 " both_signs ideal model delta sigma weight residual False 2.55 2.81 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1659 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO B 491 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO A 277 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 78 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 79 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " 0.017 5.00e-02 4.00e+02 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3309 2.82 - 3.34: 9455 3.34 - 3.86: 17341 3.86 - 4.38: 19408 4.38 - 4.90: 34766 Nonbonded interactions: 84279 Sorted by model distance: nonbonded pdb=" NE ARG A 550 " pdb=" O LEU B 434 " model vdw 2.305 2.520 nonbonded pdb=" ND2 ASN A 296 " pdb=" OD2 ASP A 299 " model vdw 2.306 2.520 nonbonded pdb=" O SER A 46 " pdb=" OG SER A 46 " model vdw 2.310 2.440 nonbonded pdb=" O GLU A 315 " pdb=" OG SER A 319 " model vdw 2.315 2.440 nonbonded pdb=" O ALA A 601 " pdb=" NE2 GLN A 607 " model vdw 2.315 2.520 ... (remaining 84274 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.010 Extract box with map and model: 5.390 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.850 Find NCS groups from input model: 0.330 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.003 0.069 10760 Z= 0.170 Angle : 0.571 10.099 14569 Z= 0.313 Chirality : 0.041 0.445 1662 Planarity : 0.003 0.039 1827 Dihedral : 13.808 87.589 3973 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.39 % Allowed : 18.58 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -1.64 (0.21), residues: 1308 helix: -0.04 (0.19), residues: 675 sheet: -0.90 (0.33), residues: 185 loop : -2.75 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 584 HIS 0.003 0.000 HIS A 470 PHE 0.007 0.001 PHE B 493 TYR 0.009 0.001 TYR B 507 ARG 0.001 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 229 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 112 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7153 (pt0) REVERT: A 114 TYR cc_start: 0.8290 (m-80) cc_final: 0.6925 (m-80) REVERT: A 118 ARG cc_start: 0.7274 (mpt180) cc_final: 0.6894 (mmt90) REVERT: A 169 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7437 (mm-30) REVERT: A 224 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7354 (p0) REVERT: A 302 MET cc_start: 0.7524 (mmm) cc_final: 0.7225 (tpp) REVERT: A 387 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7358 (mp) REVERT: B 89 GLN cc_start: 0.8371 (mt0) cc_final: 0.7729 (mp10) REVERT: B 94 LYS cc_start: 0.8581 (tttm) cc_final: 0.8360 (tptm) REVERT: B 267 ILE cc_start: 0.8736 (mt) cc_final: 0.8458 (pt) REVERT: B 281 ASP cc_start: 0.8360 (t0) cc_final: 0.8032 (t0) REVERT: B 309 TYR cc_start: 0.8340 (m-80) cc_final: 0.8123 (m-80) REVERT: B 404 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7232 (mtm110) REVERT: B 459 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (tp) REVERT: B 517 TRP cc_start: 0.6979 (m100) cc_final: 0.6372 (t60) REVERT: C 80 ASP cc_start: 0.8443 (t0) cc_final: 0.8135 (t0) REVERT: C 99 ILE cc_start: 0.8604 (mt) cc_final: 0.8313 (mp) REVERT: C 130 GLN cc_start: 0.8066 (mp-120) cc_final: 0.7774 (pp30) REVERT: D 78 VAL cc_start: 0.8061 (p) cc_final: 0.7751 (t) REVERT: D 101 GLU cc_start: 0.6566 (mp0) cc_final: 0.6044 (mp0) outliers start: 39 outliers final: 3 residues processed: 259 average time/residue: 1.1681 time to fit residues: 325.6363 Evaluate side-chains 146 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 160 ASN A 206 GLN A 392 GLN A 437 ASN A 459 GLN A 462 GLN A 578 ASN A 604 GLN A 607 GLN B 99 GLN B 131 GLN B 150 HIS B 199 GLN B 249 HIS B 409 ASN B 438 HIS B 462 ASN C 58 GLN C 75 ASN C 105 ASN C 130 GLN D 26 GLN D 47 GLN D 57 GLN D 58 GLN D 65 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 10760 Z= 0.582 Angle : 0.768 8.405 14569 Z= 0.394 Chirality : 0.050 0.187 1662 Planarity : 0.006 0.066 1827 Dihedral : 5.564 52.828 1533 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 5.47 % Allowed : 18.84 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.70 (0.23), residues: 1308 helix: 0.65 (0.20), residues: 674 sheet: -0.52 (0.35), residues: 188 loop : -2.13 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 584 HIS 0.012 0.002 HIS A 510 PHE 0.031 0.003 PHE A 642 TYR 0.024 0.002 TYR A 581 ARG 0.010 0.001 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 148 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7187 (mpt180) cc_final: 0.6699 (mpt-90) REVERT: A 169 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7775 (mm-30) REVERT: A 251 GLN cc_start: 0.8282 (mt0) cc_final: 0.7989 (OUTLIER) REVERT: A 270 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 343 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7902 (tm-30) REVERT: A 353 MET cc_start: 0.6051 (pmm) cc_final: 0.5841 (pmm) REVERT: A 383 LYS cc_start: 0.7433 (mppt) cc_final: 0.6874 (mmtm) REVERT: A 387 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7857 (mp) REVERT: A 454 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7473 (mm-40) REVERT: A 480 MET cc_start: 0.8379 (tpp) cc_final: 0.8152 (mmm) REVERT: A 481 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 536 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8176 (tp) REVERT: A 599 MET cc_start: 0.5534 (OUTLIER) cc_final: 0.5235 (mtm) REVERT: B 43 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: B 89 GLN cc_start: 0.8434 (mt0) cc_final: 0.7898 (mt0) REVERT: B 94 LYS cc_start: 0.8650 (tttm) cc_final: 0.8354 (tptm) REVERT: B 142 GLN cc_start: 0.7898 (pp30) cc_final: 0.7610 (tm-30) REVERT: B 309 TYR cc_start: 0.8362 (m-80) cc_final: 0.8144 (m-80) REVERT: B 404 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7287 (mtm110) REVERT: B 517 TRP cc_start: 0.7243 (m100) cc_final: 0.6952 (t60) REVERT: B 582 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.7019 (p) REVERT: B 628 LYS cc_start: 0.7202 (pmtt) cc_final: 0.6916 (pmtt) REVERT: B 668 LYS cc_start: 0.8139 (tptt) cc_final: 0.7557 (mtpt) REVERT: C 38 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7696 (mtp180) REVERT: C 80 ASP cc_start: 0.8529 (t0) cc_final: 0.8271 (t0) REVERT: C 99 ILE cc_start: 0.8428 (mt) cc_final: 0.8047 (mp) REVERT: D 103 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8341 (tt) outliers start: 63 outliers final: 30 residues processed: 197 average time/residue: 1.2560 time to fit residues: 265.9570 Evaluate side-chains 168 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 569 SER Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 584 TRP Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10760 Z= 0.171 Angle : 0.534 6.386 14569 Z= 0.273 Chirality : 0.040 0.138 1662 Planarity : 0.004 0.046 1827 Dihedral : 4.888 53.562 1530 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.43 % Favored : 95.49 % Rotamer: Outliers : 4.08 % Allowed : 21.01 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.04 (0.23), residues: 1308 helix: 1.33 (0.20), residues: 670 sheet: -0.21 (0.36), residues: 185 loop : -1.88 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 584 HIS 0.005 0.001 HIS A 510 PHE 0.013 0.001 PHE B 493 TYR 0.010 0.001 TYR B 571 ARG 0.003 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7193 (mpt180) cc_final: 0.6609 (mpt-90) REVERT: A 169 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7721 (mm-30) REVERT: A 251 GLN cc_start: 0.8230 (mt0) cc_final: 0.7980 (mm-40) REVERT: A 270 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 353 MET cc_start: 0.6051 (pmm) cc_final: 0.5775 (pmm) REVERT: A 383 LYS cc_start: 0.7212 (mppt) cc_final: 0.6928 (mmtm) REVERT: A 454 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7531 (mm-40) REVERT: A 481 ILE cc_start: 0.7763 (tt) cc_final: 0.7476 (mt) REVERT: A 536 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 26 ARG cc_start: 0.3497 (OUTLIER) cc_final: 0.3194 (ppt170) REVERT: B 89 GLN cc_start: 0.8465 (mt0) cc_final: 0.7957 (mt0) REVERT: B 94 LYS cc_start: 0.8624 (tttm) cc_final: 0.8376 (tptm) REVERT: B 142 GLN cc_start: 0.7788 (pp30) cc_final: 0.7520 (tm-30) REVERT: B 253 LYS cc_start: 0.8286 (mttt) cc_final: 0.8040 (mtmt) REVERT: B 309 TYR cc_start: 0.8183 (m-80) cc_final: 0.7966 (m-80) REVERT: B 404 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7268 (mtm110) REVERT: B 517 TRP cc_start: 0.7199 (m100) cc_final: 0.6899 (t60) REVERT: B 577 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7023 (mmt) REVERT: B 628 LYS cc_start: 0.7168 (pmtt) cc_final: 0.6875 (pmtt) REVERT: B 668 LYS cc_start: 0.8259 (tptt) cc_final: 0.7656 (mtpt) REVERT: C 80 ASP cc_start: 0.8470 (t0) cc_final: 0.8139 (t0) REVERT: C 99 ILE cc_start: 0.8498 (mt) cc_final: 0.8122 (mp) REVERT: C 103 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7685 (mm110) REVERT: C 130 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7537 (pp30) REVERT: D 37 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7554 (pm20) outliers start: 47 outliers final: 23 residues processed: 175 average time/residue: 1.3240 time to fit residues: 248.8967 Evaluate side-chains 156 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 0.0030 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 126 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10760 Z= 0.143 Angle : 0.513 6.730 14569 Z= 0.259 Chirality : 0.039 0.138 1662 Planarity : 0.004 0.047 1827 Dihedral : 4.441 55.432 1525 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.34 % Allowed : 20.83 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.49 (0.24), residues: 1308 helix: 1.71 (0.20), residues: 669 sheet: 0.02 (0.36), residues: 191 loop : -1.72 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.012 0.001 PHE C 89 TYR 0.010 0.001 TYR B 571 ARG 0.006 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7190 (mpt180) cc_final: 0.6574 (mpt-90) REVERT: A 169 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7758 (mm-30) REVERT: A 237 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: A 251 GLN cc_start: 0.8215 (mt0) cc_final: 0.7963 (mm-40) REVERT: A 270 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 311 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 353 MET cc_start: 0.6068 (pmm) cc_final: 0.5833 (pmm) REVERT: A 383 LYS cc_start: 0.7151 (mppt) cc_final: 0.6749 (mmtm) REVERT: A 387 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7796 (mp) REVERT: A 454 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: A 536 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8116 (tp) REVERT: B 89 GLN cc_start: 0.8507 (mt0) cc_final: 0.8010 (mt0) REVERT: B 94 LYS cc_start: 0.8599 (tttm) cc_final: 0.8379 (tptm) REVERT: B 142 GLN cc_start: 0.7692 (pp30) cc_final: 0.7288 (tm-30) REVERT: B 214 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 253 LYS cc_start: 0.8297 (mttt) cc_final: 0.8048 (mtmt) REVERT: B 287 THR cc_start: 0.8731 (m) cc_final: 0.8530 (p) REVERT: B 309 TYR cc_start: 0.8176 (m-80) cc_final: 0.7964 (m-80) REVERT: B 404 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7253 (mtm110) REVERT: B 517 TRP cc_start: 0.7217 (m100) cc_final: 0.6882 (t60) REVERT: B 668 LYS cc_start: 0.8267 (tptt) cc_final: 0.7636 (mtpt) REVERT: C 80 ASP cc_start: 0.8486 (t0) cc_final: 0.8182 (t0) REVERT: C 99 ILE cc_start: 0.8532 (mt) cc_final: 0.8168 (mp) REVERT: C 103 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7719 (mm110) REVERT: C 130 GLN cc_start: 0.7812 (pt0) cc_final: 0.7501 (pp30) REVERT: D 37 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: D 80 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8442 (mppt) outliers start: 50 outliers final: 20 residues processed: 175 average time/residue: 1.2822 time to fit residues: 240.9401 Evaluate side-chains 157 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10760 Z= 0.320 Angle : 0.610 6.773 14569 Z= 0.312 Chirality : 0.043 0.194 1662 Planarity : 0.004 0.048 1827 Dihedral : 4.698 50.489 1523 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 4.95 % Allowed : 19.79 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.38 (0.24), residues: 1308 helix: 1.48 (0.20), residues: 676 sheet: 0.10 (0.37), residues: 188 loop : -1.62 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 584 HIS 0.008 0.001 HIS A 510 PHE 0.019 0.002 PHE B 493 TYR 0.014 0.002 TYR A 581 ARG 0.007 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 134 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7266 (mpt180) cc_final: 0.6804 (mpt-90) REVERT: A 133 LEU cc_start: 0.9193 (mm) cc_final: 0.8960 (mt) REVERT: A 169 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7855 (mm-30) REVERT: A 251 GLN cc_start: 0.8256 (mt0) cc_final: 0.8035 (mm-40) REVERT: A 270 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 383 LYS cc_start: 0.7354 (mppt) cc_final: 0.6917 (mmtm) REVERT: A 387 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7855 (mp) REVERT: A 454 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7503 (mm-40) REVERT: A 536 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8133 (tp) REVERT: B 89 GLN cc_start: 0.8501 (mt0) cc_final: 0.7988 (mt0) REVERT: B 94 LYS cc_start: 0.8654 (tttm) cc_final: 0.8364 (tptm) REVERT: B 142 GLN cc_start: 0.7780 (pp30) cc_final: 0.7416 (tm-30) REVERT: B 287 THR cc_start: 0.8823 (m) cc_final: 0.8607 (p) REVERT: B 309 TYR cc_start: 0.8252 (m-80) cc_final: 0.8002 (m-80) REVERT: B 404 ARG cc_start: 0.7722 (mtp-110) cc_final: 0.7340 (mtm110) REVERT: B 429 MET cc_start: 0.7651 (ptm) cc_final: 0.7253 (mmt) REVERT: B 517 TRP cc_start: 0.7198 (m100) cc_final: 0.6880 (t60) REVERT: B 668 LYS cc_start: 0.8277 (tptt) cc_final: 0.7686 (mtpt) REVERT: C 80 ASP cc_start: 0.8485 (t0) cc_final: 0.8205 (t0) REVERT: C 103 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7642 (mm110) REVERT: C 130 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7556 (pp30) REVERT: D 37 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7546 (pm20) outliers start: 57 outliers final: 32 residues processed: 178 average time/residue: 1.2365 time to fit residues: 237.1832 Evaluate side-chains 165 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 127 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10760 Z= 0.185 Angle : 0.547 8.671 14569 Z= 0.276 Chirality : 0.041 0.173 1662 Planarity : 0.004 0.047 1827 Dihedral : 4.534 52.640 1523 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.47 % Allowed : 21.09 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.66 (0.24), residues: 1308 helix: 1.79 (0.20), residues: 668 sheet: 0.21 (0.36), residues: 192 loop : -1.59 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 584 HIS 0.006 0.001 HIS A 510 PHE 0.017 0.001 PHE C 89 TYR 0.011 0.001 TYR B 571 ARG 0.004 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7153 (mpt180) cc_final: 0.6678 (mpt-90) REVERT: A 169 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7880 (mm-30) REVERT: A 237 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7778 (tp30) REVERT: A 251 GLN cc_start: 0.8209 (mt0) cc_final: 0.8004 (mm-40) REVERT: A 270 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 343 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 383 LYS cc_start: 0.7258 (mppt) cc_final: 0.6875 (mmtm) REVERT: A 387 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 454 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: A 536 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8092 (tp) REVERT: B 89 GLN cc_start: 0.8547 (mt0) cc_final: 0.8075 (mt0) REVERT: B 94 LYS cc_start: 0.8634 (tttm) cc_final: 0.8371 (tptm) REVERT: B 142 GLN cc_start: 0.7751 (pp30) cc_final: 0.7387 (tm-30) REVERT: B 214 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7652 (p) REVERT: B 253 LYS cc_start: 0.8325 (mttt) cc_final: 0.8064 (mtmt) REVERT: B 287 THR cc_start: 0.8763 (m) cc_final: 0.8496 (p) REVERT: B 309 TYR cc_start: 0.8181 (m-80) cc_final: 0.7932 (m-80) REVERT: B 404 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7258 (mtm110) REVERT: B 429 MET cc_start: 0.7452 (ptm) cc_final: 0.7208 (mmt) REVERT: B 517 TRP cc_start: 0.7188 (m100) cc_final: 0.6868 (t60) REVERT: B 668 LYS cc_start: 0.8289 (tptt) cc_final: 0.7713 (mtpt) REVERT: C 80 ASP cc_start: 0.8480 (t0) cc_final: 0.8181 (t0) REVERT: C 130 GLN cc_start: 0.7920 (pt0) cc_final: 0.7444 (pp30) REVERT: D 37 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7587 (pm20) outliers start: 40 outliers final: 28 residues processed: 162 average time/residue: 1.2704 time to fit residues: 221.5643 Evaluate side-chains 159 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN C 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10760 Z= 0.369 Angle : 0.632 7.022 14569 Z= 0.324 Chirality : 0.044 0.173 1662 Planarity : 0.004 0.048 1827 Dihedral : 4.805 49.820 1523 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 4.60 % Allowed : 19.79 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.44 (0.24), residues: 1308 helix: 1.50 (0.20), residues: 676 sheet: 0.12 (0.36), residues: 194 loop : -1.55 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 584 HIS 0.009 0.002 HIS A 510 PHE 0.020 0.002 PHE B 493 TYR 0.014 0.002 TYR D 111 ARG 0.006 0.001 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 132 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7196 (mpt180) cc_final: 0.6795 (mpt-90) REVERT: A 133 LEU cc_start: 0.9184 (mm) cc_final: 0.8958 (mt) REVERT: A 169 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7949 (mm-30) REVERT: A 251 GLN cc_start: 0.8274 (mt0) cc_final: 0.8047 (mm-40) REVERT: A 343 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 383 LYS cc_start: 0.7384 (mppt) cc_final: 0.6972 (mmtm) REVERT: A 387 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 454 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7494 (mm-40) REVERT: A 536 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8102 (tp) REVERT: A 599 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.4609 (mtt) REVERT: B 89 GLN cc_start: 0.8524 (mt0) cc_final: 0.8033 (mt0) REVERT: B 94 LYS cc_start: 0.8676 (tttm) cc_final: 0.8464 (tptp) REVERT: B 142 GLN cc_start: 0.7775 (pp30) cc_final: 0.7423 (tm-30) REVERT: B 253 LYS cc_start: 0.8347 (mttt) cc_final: 0.8077 (mtmt) REVERT: B 287 THR cc_start: 0.8785 (m) cc_final: 0.8502 (p) REVERT: B 309 TYR cc_start: 0.8219 (m-80) cc_final: 0.7950 (m-80) REVERT: B 404 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7344 (mtm110) REVERT: B 517 TRP cc_start: 0.7173 (m100) cc_final: 0.6867 (t60) REVERT: B 668 LYS cc_start: 0.8311 (tptt) cc_final: 0.7737 (mtpt) REVERT: C 80 ASP cc_start: 0.8533 (t0) cc_final: 0.8256 (t0) REVERT: C 99 ILE cc_start: 0.8536 (mt) cc_final: 0.8147 (mp) outliers start: 53 outliers final: 36 residues processed: 173 average time/residue: 1.2579 time to fit residues: 234.4966 Evaluate side-chains 165 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 ASN B 607 GLN C 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10760 Z= 0.161 Angle : 0.538 8.416 14569 Z= 0.271 Chirality : 0.040 0.170 1662 Planarity : 0.004 0.049 1827 Dihedral : 4.539 52.734 1523 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.08 % Allowed : 20.83 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.79 (0.24), residues: 1308 helix: 1.89 (0.20), residues: 669 sheet: 0.21 (0.35), residues: 200 loop : -1.52 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 536 HIS 0.005 0.001 HIS B 531 PHE 0.014 0.001 PHE A 502 TYR 0.010 0.001 TYR B 571 ARG 0.004 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 131 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7122 (mpt180) cc_final: 0.6736 (mpt-90) REVERT: A 169 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7910 (mm-30) REVERT: A 237 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: A 251 GLN cc_start: 0.8174 (mt0) cc_final: 0.7957 (mm-40) REVERT: A 270 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 343 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7709 (tm-30) REVERT: A 383 LYS cc_start: 0.7251 (mppt) cc_final: 0.7036 (mmtm) REVERT: A 454 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: A 536 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8090 (tp) REVERT: B 89 GLN cc_start: 0.8579 (mt0) cc_final: 0.8121 (mt0) REVERT: B 94 LYS cc_start: 0.8639 (tttm) cc_final: 0.8361 (tptm) REVERT: B 142 GLN cc_start: 0.7754 (pp30) cc_final: 0.7407 (tm-30) REVERT: B 214 SER cc_start: 0.7896 (OUTLIER) cc_final: 0.7627 (p) REVERT: B 253 LYS cc_start: 0.8327 (mttt) cc_final: 0.8067 (mtmt) REVERT: B 287 THR cc_start: 0.8767 (m) cc_final: 0.8552 (p) REVERT: B 309 TYR cc_start: 0.8141 (m-80) cc_final: 0.7897 (m-80) REVERT: B 404 ARG cc_start: 0.7694 (mtp-110) cc_final: 0.7273 (mtm110) REVERT: B 517 TRP cc_start: 0.7163 (m100) cc_final: 0.6870 (t60) REVERT: B 668 LYS cc_start: 0.8304 (tptt) cc_final: 0.7750 (mtpt) REVERT: C 80 ASP cc_start: 0.8485 (t0) cc_final: 0.8172 (t0) REVERT: C 99 ILE cc_start: 0.8543 (mt) cc_final: 0.8138 (mp) REVERT: C 130 GLN cc_start: 0.7804 (pt0) cc_final: 0.7581 (pp30) REVERT: D 37 GLU cc_start: 0.7890 (mp0) cc_final: 0.7611 (pm20) outliers start: 47 outliers final: 28 residues processed: 169 average time/residue: 1.2565 time to fit residues: 228.7601 Evaluate side-chains 158 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10760 Z= 0.157 Angle : 0.526 9.176 14569 Z= 0.264 Chirality : 0.040 0.162 1662 Planarity : 0.004 0.052 1827 Dihedral : 4.409 54.622 1523 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.21 % Allowed : 21.88 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1308 helix: 2.05 (0.20), residues: 670 sheet: 0.38 (0.36), residues: 201 loop : -1.36 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 229 HIS 0.005 0.001 HIS B 531 PHE 0.013 0.001 PHE A 502 TYR 0.010 0.001 TYR B 571 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7098 (mpt180) cc_final: 0.6713 (mpt-90) REVERT: A 237 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: A 251 GLN cc_start: 0.8183 (mt0) cc_final: 0.7968 (mm-40) REVERT: A 270 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 343 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 383 LYS cc_start: 0.7247 (mppt) cc_final: 0.6877 (mmtm) REVERT: A 454 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7529 (mm-40) REVERT: A 536 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 89 GLN cc_start: 0.8589 (mt0) cc_final: 0.8148 (mt0) REVERT: B 94 LYS cc_start: 0.8657 (tttm) cc_final: 0.8416 (tptm) REVERT: B 214 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7594 (p) REVERT: B 253 LYS cc_start: 0.8327 (mttt) cc_final: 0.8068 (mtmt) REVERT: B 309 TYR cc_start: 0.8156 (m-80) cc_final: 0.7858 (m-80) REVERT: B 404 ARG cc_start: 0.7657 (mtp-110) cc_final: 0.7233 (mtm110) REVERT: B 517 TRP cc_start: 0.7174 (m100) cc_final: 0.6823 (t60) REVERT: B 668 LYS cc_start: 0.8332 (tptt) cc_final: 0.7738 (mtpt) REVERT: C 80 ASP cc_start: 0.8465 (t0) cc_final: 0.8177 (t0) REVERT: D 80 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8422 (mppt) outliers start: 37 outliers final: 27 residues processed: 165 average time/residue: 1.2136 time to fit residues: 215.4658 Evaluate side-chains 157 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.0470 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 103 optimal weight: 0.1980 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10760 Z= 0.201 Angle : 0.554 8.643 14569 Z= 0.280 Chirality : 0.041 0.159 1662 Planarity : 0.004 0.051 1827 Dihedral : 4.476 53.751 1523 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.47 % Allowed : 21.53 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1308 helix: 2.02 (0.20), residues: 671 sheet: 0.42 (0.36), residues: 202 loop : -1.36 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 229 HIS 0.006 0.001 HIS A 510 PHE 0.015 0.001 PHE B 493 TYR 0.011 0.001 TYR B 571 ARG 0.004 0.000 ARG A 550 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 118 ARG cc_start: 0.7100 (mpt180) cc_final: 0.6711 (mpt-90) REVERT: A 237 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: A 251 GLN cc_start: 0.8215 (mt0) cc_final: 0.7985 (mm-40) REVERT: A 270 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 343 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7662 (tm-30) REVERT: A 454 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: A 536 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8116 (tp) REVERT: B 26 ARG cc_start: 0.3778 (OUTLIER) cc_final: 0.3292 (ppt-90) REVERT: B 89 GLN cc_start: 0.8577 (mt0) cc_final: 0.8141 (mt0) REVERT: B 94 LYS cc_start: 0.8651 (tttm) cc_final: 0.8407 (tptm) REVERT: B 214 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7670 (p) REVERT: B 253 LYS cc_start: 0.8333 (mttt) cc_final: 0.8070 (mtmt) REVERT: B 309 TYR cc_start: 0.8165 (m-80) cc_final: 0.7863 (m-80) REVERT: B 404 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7257 (mtm110) REVERT: B 517 TRP cc_start: 0.7195 (m100) cc_final: 0.6806 (t60) REVERT: B 668 LYS cc_start: 0.8329 (tptt) cc_final: 0.7736 (mtpt) REVERT: C 80 ASP cc_start: 0.8485 (t0) cc_final: 0.8195 (t0) REVERT: D 80 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8424 (mppt) outliers start: 40 outliers final: 30 residues processed: 160 average time/residue: 1.2982 time to fit residues: 223.1361 Evaluate side-chains 158 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 629 SER Chi-restraints excluded: chain B residue 26 ARG Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 HIS B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.081960 restraints weight = 14693.008| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.06 r_work: 0.2723 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10760 Z= 0.152 Angle : 0.518 8.381 14569 Z= 0.262 Chirality : 0.039 0.159 1662 Planarity : 0.004 0.050 1827 Dihedral : 4.360 55.522 1523 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.12 % Allowed : 21.61 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.19 (0.24), residues: 1308 helix: 2.19 (0.20), residues: 668 sheet: 0.51 (0.36), residues: 201 loop : -1.36 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 536 HIS 0.005 0.001 HIS B 531 PHE 0.013 0.001 PHE A 502 TYR 0.010 0.001 TYR B 571 ARG 0.003 0.000 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4321.33 seconds wall clock time: 77 minutes 18.38 seconds (4638.38 seconds total)