Starting phenix.real_space_refine on Tue Feb 13 07:28:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/02_2024/8hnb_34909.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/02_2024/8hnb_34909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/02_2024/8hnb_34909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/02_2024/8hnb_34909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/02_2024/8hnb_34909.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnb_34909/02_2024/8hnb_34909.pdb" } resolution = 3.53 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= 0.021 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 32 5.16 5 C 2689 2.51 5 N 649 2.21 5 O 713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4083 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4041 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 3 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 189 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.67 Number of scatterers: 4083 At special positions: 0 Unit cell: (101.504, 59.072, 79.872, 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 32 16.00 O 713 8.00 N 649 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.04 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.04 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.02 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 790.0 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 69.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 26 through 60 removed outlier: 4.140A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 removed outlier: 3.900A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.794A pdb=" N LEU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.588A pdb=" N MET A 118 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.546A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.596A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 180 " --> pdb=" O MET A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.971A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.782A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 Processing helix chain 'A' and resid 257 through 273 removed outlier: 3.516A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.923A pdb=" N PHE A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.212A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 401 removed outlier: 3.846A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.571A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.131A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.515A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.710A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 removed outlier: 3.597A pdb=" N LEU A 582 " --> pdb=" O VAL A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 4.442A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 6.594A pdb=" N PHE A 501 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER A 492 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 503 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 602 removed outlier: 7.059A pdb=" N THR A 615 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP A 602 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS A 613 " --> pdb=" O TRP A 602 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 768 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: 1.14 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 744 1.33 - 1.45: 1084 1.45 - 1.57: 2302 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 4178 Sorted by residual: bond pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 1.409 1.481 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA ALA A 581 " pdb=" C ALA A 581 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.75e+00 bond pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 1.520 1.557 -0.037 1.26e-02 6.30e+03 8.62e+00 bond pdb=" C GLN A 369 " pdb=" N PRO A 370 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.08e-02 8.57e+03 8.23e+00 bond pdb=" C TYR A 640 " pdb=" O TYR A 640 " ideal model delta sigma weight residual 1.236 1.205 0.032 1.15e-02 7.56e+03 7.57e+00 ... (remaining 4173 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.14: 76 105.14 - 112.37: 2003 112.37 - 119.60: 1404 119.60 - 126.83: 2152 126.83 - 134.06: 41 Bond angle restraints: 5676 Sorted by residual: angle pdb=" N TYR A 121 " pdb=" CA TYR A 121 " pdb=" C TYR A 121 " ideal model delta sigma weight residual 109.15 98.24 10.91 1.44e+00 4.82e-01 5.74e+01 angle pdb=" N PHE A 591 " pdb=" CA PHE A 591 " pdb=" C PHE A 591 " ideal model delta sigma weight residual 111.14 104.03 7.11 1.08e+00 8.57e-01 4.33e+01 angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" C GLU A 364 " ideal model delta sigma weight residual 111.36 118.51 -7.15 1.09e+00 8.42e-01 4.30e+01 angle pdb=" N LEU A 113 " pdb=" CA LEU A 113 " pdb=" C LEU A 113 " ideal model delta sigma weight residual 109.81 123.05 -13.24 2.21e+00 2.05e-01 3.59e+01 angle pdb=" N TYR A 502 " pdb=" CA TYR A 502 " pdb=" C TYR A 502 " ideal model delta sigma weight residual 110.42 119.66 -9.24 1.55e+00 4.16e-01 3.55e+01 ... (remaining 5671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.06: 2303 21.06 - 42.12: 133 42.12 - 63.18: 16 63.18 - 84.24: 2 84.24 - 105.30: 8 Dihedral angle restraints: 2462 sinusoidal: 861 harmonic: 1601 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -129.16 43.16 1 1.00e+01 1.00e-02 2.60e+01 dihedral pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual 123.40 135.31 -11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" C ILE A 407 " pdb=" N ILE A 407 " pdb=" CA ILE A 407 " pdb=" CB ILE A 407 " ideal model delta harmonic sigma weight residual -122.00 -133.65 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 2459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 523 0.083 - 0.166: 114 0.166 - 0.249: 23 0.249 - 0.332: 8 0.332 - 0.415: 5 Chirality restraints: 673 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA SER A 140 " pdb=" N SER A 140 " pdb=" C SER A 140 " pdb=" CB SER A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 670 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 701 " -0.290 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG A 701 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 701 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG A 701 " 0.415 2.00e-02 2.50e+03 pdb=" O7 NAG A 701 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.140 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" C7 NAG B 1 " -0.029 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 1748 2.89 - 3.39: 4409 3.39 - 3.89: 6500 3.89 - 4.40: 7456 4.40 - 4.90: 12134 Nonbonded interactions: 32247 Sorted by model distance: nonbonded pdb=" O SER A 140 " pdb=" N CYS A 485 " model vdw 2.382 2.520 nonbonded pdb=" O3 NAG B 1 " pdb=" O5 NAG B 2 " model vdw 2.455 2.440 nonbonded pdb=" OG SER A 328 " pdb=" CD2 LEU A 570 " model vdw 2.458 3.460 nonbonded pdb=" N GLY A 223 " pdb=" N PHE A 224 " model vdw 2.460 2.560 nonbonded pdb=" N SER A 457 " pdb=" O SER A 457 " model vdw 2.496 2.496 ... (remaining 32242 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 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.580 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.007 0.072 4178 Z= 0.446 Angle : 1.349 13.238 5676 Z= 0.919 Chirality : 0.083 0.415 673 Planarity : 0.016 0.261 698 Dihedral : 14.650 105.302 1421 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.09 % Allowed : 9.92 % Favored : 87.99 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % 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 (0.33), residues: 554 helix: 0.20 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -1.42 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 259 HIS 0.003 0.001 HIS A 575 PHE 0.014 0.001 PHE A 574 TYR 0.025 0.002 TYR A 338 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.436 Fit side-chains REVERT: A 48 MET cc_start: 0.8622 (tpt) cc_final: 0.8343 (tpt) REVERT: A 115 HIS cc_start: 0.7412 (t-90) cc_final: 0.7135 (t-90) REVERT: A 332 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6262 (mm) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 0.1801 time to fit residues: 27.1989 Evaluate side-chains 88 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 366 GLN A 541 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4178 Z= 0.228 Angle : 0.735 10.678 5676 Z= 0.354 Chirality : 0.043 0.242 673 Planarity : 0.004 0.030 698 Dihedral : 8.428 59.967 656 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.13 % Allowed : 16.97 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.34), residues: 554 helix: 1.22 (0.27), residues: 340 sheet: -5.39 (0.52), residues: 5 loop : -1.14 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.004 0.001 HIS A 204 PHE 0.013 0.001 PHE A 73 TYR 0.020 0.002 TYR A 338 ARG 0.007 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8246 (mtm180) cc_final: 0.7878 (mtm-85) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.1806 time to fit residues: 23.1129 Evaluate side-chains 92 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 579 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.0000 chunk 34 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4178 Z= 0.202 Angle : 0.671 9.780 5676 Z= 0.325 Chirality : 0.040 0.226 673 Planarity : 0.004 0.032 698 Dihedral : 6.206 58.548 654 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.18 % Allowed : 19.06 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.35), residues: 554 helix: 1.58 (0.27), residues: 343 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 602 HIS 0.016 0.003 HIS A 115 PHE 0.013 0.001 PHE A 73 TYR 0.040 0.002 TYR A 590 ARG 0.008 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 27 LEU cc_start: 0.6993 (tt) cc_final: 0.6503 (tt) REVERT: A 48 MET cc_start: 0.8667 (tpt) cc_final: 0.8451 (tpt) outliers start: 16 outliers final: 7 residues processed: 109 average time/residue: 0.1790 time to fit residues: 23.6969 Evaluate side-chains 97 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 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 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4178 Z= 0.231 Angle : 0.648 9.434 5676 Z= 0.313 Chirality : 0.041 0.219 673 Planarity : 0.004 0.037 698 Dihedral : 5.529 55.816 654 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.48 % Allowed : 18.28 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.35), residues: 554 helix: 1.65 (0.27), residues: 342 sheet: None (None), residues: 0 loop : -0.69 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 602 HIS 0.010 0.002 HIS A 115 PHE 0.012 0.001 PHE A 73 TYR 0.044 0.002 TYR A 590 ARG 0.009 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.405 Fit side-chains REVERT: A 48 MET cc_start: 0.8711 (tpt) cc_final: 0.8417 (tpt) REVERT: A 577 MET cc_start: 0.7632 (ttp) cc_final: 0.7401 (ttp) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.1824 time to fit residues: 22.9390 Evaluate side-chains 99 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4178 Z= 0.214 Angle : 0.648 9.426 5676 Z= 0.311 Chirality : 0.040 0.204 673 Planarity : 0.004 0.038 698 Dihedral : 5.394 55.825 654 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.66 % Allowed : 20.37 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.35), residues: 554 helix: 1.83 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 259 HIS 0.002 0.001 HIS A 575 PHE 0.012 0.001 PHE A 73 TYR 0.036 0.002 TYR A 590 ARG 0.010 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.593 Fit side-chains REVERT: A 48 MET cc_start: 0.8675 (tpt) cc_final: 0.8459 (tpt) REVERT: A 577 MET cc_start: 0.7742 (ttp) cc_final: 0.7404 (ttt) outliers start: 14 outliers final: 13 residues processed: 97 average time/residue: 0.1932 time to fit residues: 22.9242 Evaluate side-chains 97 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4178 Z= 0.239 Angle : 0.658 9.444 5676 Z= 0.316 Chirality : 0.040 0.197 673 Planarity : 0.004 0.046 698 Dihedral : 5.313 55.734 654 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.44 % Allowed : 19.84 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.35), residues: 554 helix: 1.73 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 115 PHE 0.012 0.001 PHE A 73 TYR 0.035 0.002 TYR A 590 ARG 0.010 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.466 Fit side-chains REVERT: A 577 MET cc_start: 0.7805 (ttp) cc_final: 0.7521 (ttp) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.1901 time to fit residues: 22.1203 Evaluate side-chains 95 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 34 optimal weight: 0.0970 chunk 36 optimal weight: 30.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4178 Z= 0.232 Angle : 0.652 9.441 5676 Z= 0.313 Chirality : 0.040 0.190 673 Planarity : 0.004 0.051 698 Dihedral : 5.371 55.869 654 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.66 % Allowed : 22.19 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.35), residues: 554 helix: 1.72 (0.27), residues: 349 sheet: None (None), residues: 0 loop : -0.68 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.005 0.001 HIS A 115 PHE 0.017 0.001 PHE A 117 TYR 0.035 0.002 TYR A 590 ARG 0.011 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.403 Fit side-chains REVERT: A 60 GLU cc_start: 0.7435 (pp20) cc_final: 0.7072 (pm20) REVERT: A 117 PHE cc_start: 0.8308 (m-10) cc_final: 0.8107 (m-10) REVERT: A 176 MET cc_start: 0.7920 (tpp) cc_final: 0.7694 (mmm) REVERT: A 577 MET cc_start: 0.7863 (ttp) cc_final: 0.7522 (ttt) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 0.1815 time to fit residues: 21.0868 Evaluate side-chains 97 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4178 Z= 0.235 Angle : 0.672 9.441 5676 Z= 0.321 Chirality : 0.040 0.183 673 Planarity : 0.004 0.054 698 Dihedral : 5.326 55.910 654 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.87 % Allowed : 23.50 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.35), residues: 554 helix: 1.70 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.001 0.001 HIS A 204 PHE 0.020 0.001 PHE A 391 TYR 0.041 0.002 TYR A 590 ARG 0.012 0.001 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.7978 (tpp) cc_final: 0.7737 (mmm) REVERT: A 577 MET cc_start: 0.7898 (ttp) cc_final: 0.7477 (ttt) outliers start: 11 outliers final: 11 residues processed: 91 average time/residue: 0.1887 time to fit residues: 20.7903 Evaluate side-chains 92 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 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 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4178 Z= 0.236 Angle : 0.682 9.549 5676 Z= 0.326 Chirality : 0.041 0.180 673 Planarity : 0.004 0.055 698 Dihedral : 5.367 56.007 654 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.92 % Allowed : 23.76 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.35), residues: 554 helix: 1.69 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -0.46 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 254 HIS 0.001 0.001 HIS A 204 PHE 0.017 0.001 PHE A 117 TYR 0.040 0.002 TYR A 590 ARG 0.014 0.002 ARG A 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8000 (tpp) cc_final: 0.7776 (mmm) REVERT: A 577 MET cc_start: 0.7918 (ttp) cc_final: 0.7465 (ttt) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.1871 time to fit residues: 20.5802 Evaluate side-chains 94 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 120 TYR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.0030 chunk 47 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 40.0000 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.0020 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4178 Z= 0.203 Angle : 0.678 9.449 5676 Z= 0.321 Chirality : 0.040 0.182 673 Planarity : 0.004 0.062 698 Dihedral : 5.345 56.061 654 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.39 % Allowed : 23.24 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.35), residues: 554 helix: 1.77 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -0.43 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 602 HIS 0.004 0.001 HIS A 115 PHE 0.025 0.001 PHE A 391 TYR 0.041 0.002 TYR A 590 ARG 0.014 0.002 ARG A 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 176 MET cc_start: 0.8037 (tpp) cc_final: 0.7817 (mmm) REVERT: A 197 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: A 577 MET cc_start: 0.7897 (ttp) cc_final: 0.7441 (ttt) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1846 time to fit residues: 20.3545 Evaluate side-chains 92 residues out of total 485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 589 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** 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 = 0.4174 r_free = 0.4174 target = 0.187773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128964 restraints weight = 4841.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134432 restraints weight = 2371.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138064 restraints weight = 1549.694| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4178 Z= 0.233 Angle : 0.696 10.907 5676 Z= 0.324 Chirality : 0.041 0.181 673 Planarity : 0.004 0.061 698 Dihedral : 5.319 56.102 654 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.13 % Allowed : 23.76 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.35), residues: 554 helix: 1.77 (0.27), residues: 345 sheet: None (None), residues: 0 loop : -0.40 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 602 HIS 0.004 0.001 HIS A 115 PHE 0.018 0.001 PHE A 117 TYR 0.040 0.002 TYR A 590 ARG 0.014 0.002 ARG A 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1265.24 seconds wall clock time: 24 minutes 19.26 seconds (1459.26 seconds total)