Starting phenix.real_space_refine on Wed Feb 14 22:02:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q49_13799/02_2024/7q49_13799_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q49_13799/02_2024/7q49_13799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q49_13799/02_2024/7q49_13799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q49_13799/02_2024/7q49_13799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q49_13799/02_2024/7q49_13799_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q49_13799/02_2024/7q49_13799_trim.pdb" } resolution = 3.72 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= 0.003 sd= 0.059 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 19 5.16 5 C 3398 2.51 5 N 873 2.21 5 O 1045 1.98 5 H 4788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10124 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 9804 Classifications: {'peptide': 616} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 577} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.30, per 1000 atoms: 0.52 Number of scatterers: 10124 At special positions: 0 Unit cell: (77.38, 89.04, 93.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 19 16.00 O 1045 8.00 N 873 7.00 C 3398 6.00 H 4788 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 528 " 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1302 " - " ASN A 82 " " NAG A1303 " - " ASN A 416 " " NAG B 1 " - " ASN A 25 " " NAG C 1 " - " ASN A 289 " " NAG D 1 " - " ASN A 9 " " NAG E 1 " - " ASN A 117 " " NAG F 1 " - " ASN A 45 " " NAG G 1 " - " ASN A 480 " Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 365 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A 361 " 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 70.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 13 through 45 removed outlier: 3.804A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 77 removed outlier: 3.758A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 85 through 97 Processing helix chain 'A' and resid 98 through 103 removed outlier: 3.583A pdb=" N ALA A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 190 Proline residue: A 170 - end of helix Proline residue: A 173 - end of helix removed outlier: 3.644A pdb=" N GLU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.803A pdb=" N TRP A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 238 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 261 through 263 No H-bonds generated for 'chain 'A' and resid 261 through 263' Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 279 through 286 removed outlier: 3.578A pdb=" N GLN A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.620A pdb=" N ARG A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.966A pdb=" N TRP A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 373 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 386 through 401 removed outlier: 3.590A pdb=" N GLY A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 417 through 433 Processing helix chain 'A' and resid 434 through 452 removed outlier: 4.473A pdb=" N PHE A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 472 removed outlier: 3.557A pdb=" N TRP A 463 " --> pdb=" O TYR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.682A pdb=" N PHE A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 509 " --> pdb=" O PHE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.526A pdb=" N LYS A 539 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 567 through 574 Processing helix chain 'A' and resid 574 through 589 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.065A pdb=" N ILE A 248 " --> pdb=" O CYS A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 336 294 hydrogen bonds defined for protein. 843 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: 3.82 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4787 1.04 - 1.24: 587 1.24 - 1.44: 1914 1.44 - 1.63: 2960 1.63 - 1.83: 31 Bond restraints: 10279 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.358 0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sigma weight residual 1.417 1.463 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.568 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG E 2 " pdb=" C2 NAG E 2 " ideal model delta sigma weight residual 1.532 1.491 0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 3.95e+00 ... (remaining 10274 not shown) Histogram of bond angle deviations from ideal: 97.18 - 104.55: 122 104.55 - 111.93: 11077 111.93 - 119.30: 2688 119.30 - 126.67: 4350 126.67 - 134.04: 123 Bond angle restraints: 18360 Sorted by residual: angle pdb=" C LYS A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta sigma weight residual 121.62 115.31 6.31 1.83e+00 2.99e-01 1.19e+01 angle pdb=" N LYS A 321 " pdb=" CA LYS A 321 " pdb=" C LYS A 321 " ideal model delta sigma weight residual 109.81 102.50 7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" CA TYR A 338 " pdb=" CB TYR A 338 " pdb=" CG TYR A 338 " ideal model delta sigma weight residual 113.90 108.25 5.65 1.80e+00 3.09e-01 9.85e+00 angle pdb=" N THR A 349 " pdb=" CA THR A 349 " pdb=" C THR A 349 " ideal model delta sigma weight residual 110.23 114.52 -4.29 1.45e+00 4.76e-01 8.77e+00 angle pdb=" N PHE A 83 " pdb=" CA PHE A 83 " pdb=" CB PHE A 83 " ideal model delta sigma weight residual 109.48 113.98 -4.50 1.55e+00 4.16e-01 8.42e+00 ... (remaining 18355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.35: 4789 21.35 - 42.69: 288 42.69 - 64.04: 98 64.04 - 85.39: 49 85.39 - 106.73: 29 Dihedral angle restraints: 5253 sinusoidal: 2996 harmonic: 2257 Sorted by residual: dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.02 106.73 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.53 105.15 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.74 104.45 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 5250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 682 0.066 - 0.132: 146 0.132 - 0.198: 14 0.198 - 0.264: 5 0.264 - 0.330: 7 Chirality restraints: 854 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 851 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 508 " -0.046 2.00e-02 2.50e+03 5.32e-02 4.25e+01 pdb=" CD GLN A 508 " 0.050 2.00e-02 2.50e+03 pdb=" OE1 GLN A 508 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN A 508 " 0.077 2.00e-02 2.50e+03 pdb="HE21 GLN A 508 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 508 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 479 " -0.130 9.50e-02 1.11e+02 5.15e-02 1.91e+01 pdb=" NE ARG A 479 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG A 479 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 479 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 479 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 479 " -0.003 2.00e-02 2.50e+03 pdb="HH12 ARG A 479 " 0.045 2.00e-02 2.50e+03 pdb="HH21 ARG A 479 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 479 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 371 " 0.028 2.00e-02 2.50e+03 3.34e-02 1.67e+01 pdb=" CD GLN A 371 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN A 371 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 371 " -0.051 2.00e-02 2.50e+03 pdb="HE21 GLN A 371 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 371 " 0.050 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 309 2.14 - 2.76: 18476 2.76 - 3.37: 28899 3.37 - 3.99: 35865 3.99 - 4.60: 56711 Nonbonded interactions: 140260 Sorted by model distance: nonbonded pdb=" HG1 THR A 454 " pdb=" OD2 ASP A 462 " model vdw 1.526 1.850 nonbonded pdb=" HG1 THR A 468 " pdb=" O ILE A 473 " model vdw 1.531 1.850 nonbonded pdb=" HH TYR A 521 " pdb=" O PRO A 524 " model vdw 1.558 1.850 nonbonded pdb=" O TRP A 40 " pdb=" HG1 THR A 44 " model vdw 1.559 1.850 nonbonded pdb=" OD2 ASP A 443 " pdb=" H ILE A 499 " model vdw 1.594 1.850 ... (remaining 140255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 4.070 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 40.750 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 5491 Z= 0.547 Angle : 1.081 7.934 7484 Z= 0.569 Chirality : 0.061 0.330 854 Planarity : 0.009 0.105 935 Dihedral : 19.174 106.734 2370 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.19 % Allowed : 1.70 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.50 (0.30), residues: 614 helix: -0.60 (0.22), residues: 367 sheet: -0.97 (1.76), residues: 10 loop : -1.48 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.006 TRP A 257 HIS 0.010 0.003 HIS A 331 PHE 0.028 0.004 PHE A 509 TYR 0.032 0.005 TYR A 338 ARG 0.031 0.005 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.8231 (pt0) cc_final: 0.8019 (tt0) REVERT: A 52 ARG cc_start: 0.8909 (tpt170) cc_final: 0.8677 (ttp-110) REVERT: A 64 PHE cc_start: 0.7995 (t80) cc_final: 0.7661 (t80) REVERT: A 132 LYS cc_start: 0.8260 (tttt) cc_final: 0.7988 (mmmt) REVERT: A 155 MET cc_start: 0.8060 (tpt) cc_final: 0.7768 (tpt) REVERT: A 156 LEU cc_start: 0.9086 (tp) cc_final: 0.8769 (tp) REVERT: A 182 SER cc_start: 0.9198 (t) cc_final: 0.8765 (m) REVERT: A 183 ASN cc_start: 0.8341 (m-40) cc_final: 0.8080 (t0) REVERT: A 298 GLU cc_start: 0.8454 (tt0) cc_final: 0.7972 (tm-30) REVERT: A 302 THR cc_start: 0.9124 (p) cc_final: 0.8425 (p) REVERT: A 341 LYS cc_start: 0.7998 (mttt) cc_final: 0.7673 (mmpt) REVERT: A 350 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7386 (ttm170) REVERT: A 453 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6909 (tmm160) REVERT: A 579 GLN cc_start: 0.7818 (tt0) cc_final: 0.7450 (tm-30) REVERT: A 592 LEU cc_start: 0.8423 (mt) cc_final: 0.8166 (pt) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.4494 time to fit residues: 68.7221 Evaluate side-chains 81 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 216 GLN A 292 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN A 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5491 Z= 0.244 Angle : 0.784 10.502 7484 Z= 0.403 Chirality : 0.045 0.209 854 Planarity : 0.005 0.046 935 Dihedral : 13.467 68.881 1180 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.32 % Allowed : 9.43 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.32), residues: 614 helix: 0.59 (0.25), residues: 378 sheet: None (None), residues: 0 loop : -0.78 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 552 HIS 0.010 0.002 HIS A 360 PHE 0.029 0.002 PHE A 294 TYR 0.018 0.002 TYR A 215 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8899 (tpt170) cc_final: 0.8661 (ttp-110) REVERT: A 182 SER cc_start: 0.9114 (t) cc_final: 0.8820 (m) REVERT: A 183 ASN cc_start: 0.8384 (m-40) cc_final: 0.7954 (t0) REVERT: A 283 MET cc_start: 0.8579 (ttp) cc_final: 0.8358 (ttp) REVERT: A 298 GLU cc_start: 0.8314 (tt0) cc_final: 0.8083 (tm-30) REVERT: A 350 ARG cc_start: 0.7410 (ttt180) cc_final: 0.7188 (ttt90) REVERT: A 379 LEU cc_start: 0.8210 (mt) cc_final: 0.7930 (mt) REVERT: A 453 ARG cc_start: 0.7310 (mtt90) cc_final: 0.6967 (tmm160) REVERT: A 582 GLN cc_start: 0.8055 (mt0) cc_final: 0.7596 (tp40) REVERT: A 592 LEU cc_start: 0.8408 (mt) cc_final: 0.8170 (pt) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.4610 time to fit residues: 59.4259 Evaluate side-chains 88 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5491 Z= 0.213 Angle : 0.665 5.789 7484 Z= 0.340 Chirality : 0.041 0.190 854 Planarity : 0.005 0.048 935 Dihedral : 9.681 60.870 1180 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.32 % Allowed : 11.70 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.76 (0.33), residues: 614 helix: 1.00 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.18 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.012 0.002 HIS A 251 PHE 0.015 0.002 PHE A 294 TYR 0.016 0.002 TYR A 368 ARG 0.003 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6458 (tt) REVERT: A 182 SER cc_start: 0.9066 (t) cc_final: 0.8820 (m) REVERT: A 183 ASN cc_start: 0.8437 (m-40) cc_final: 0.7997 (t0) REVERT: A 189 ASP cc_start: 0.8611 (t0) cc_final: 0.8056 (t70) REVERT: A 215 TYR cc_start: 0.6954 (t80) cc_final: 0.6622 (t80) REVERT: A 298 GLU cc_start: 0.8419 (tt0) cc_final: 0.8209 (tm-30) REVERT: A 338 TYR cc_start: 0.9201 (m-80) cc_final: 0.8991 (m-10) REVERT: A 379 LEU cc_start: 0.8220 (mt) cc_final: 0.8001 (mt) REVERT: A 453 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7008 (tmm160) REVERT: A 582 GLN cc_start: 0.8025 (mt0) cc_final: 0.7520 (tp40) REVERT: A 592 LEU cc_start: 0.8409 (mt) cc_final: 0.8137 (pt) outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.4381 time to fit residues: 51.4620 Evaluate side-chains 85 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5491 Z= 0.178 Angle : 0.588 5.631 7484 Z= 0.302 Chirality : 0.038 0.185 854 Planarity : 0.004 0.047 935 Dihedral : 7.702 59.792 1180 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.89 % Allowed : 12.08 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.09 (0.34), residues: 614 helix: 1.30 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.10 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.010 0.001 HIS A 251 PHE 0.011 0.001 PHE A 178 TYR 0.014 0.001 TYR A 372 ARG 0.002 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9006 (tp) cc_final: 0.8701 (tp) REVERT: A 182 SER cc_start: 0.9038 (t) cc_final: 0.8817 (m) REVERT: A 183 ASN cc_start: 0.8394 (m-40) cc_final: 0.7683 (t0) REVERT: A 189 ASP cc_start: 0.8736 (t0) cc_final: 0.8206 (t70) REVERT: A 215 TYR cc_start: 0.6851 (t80) cc_final: 0.6522 (t80) REVERT: A 262 GLU cc_start: 0.7741 (tt0) cc_final: 0.6946 (tp30) REVERT: A 298 GLU cc_start: 0.8451 (tt0) cc_final: 0.8196 (tm-30) REVERT: A 309 MET cc_start: 0.8880 (mmp) cc_final: 0.8558 (mmp) REVERT: A 338 TYR cc_start: 0.9215 (m-80) cc_final: 0.8968 (m-10) REVERT: A 431 GLU cc_start: 0.7613 (tt0) cc_final: 0.7255 (tp30) REVERT: A 453 ARG cc_start: 0.7458 (mtt90) cc_final: 0.6988 (tmm160) REVERT: A 582 GLN cc_start: 0.8013 (mt0) cc_final: 0.7526 (tp40) REVERT: A 592 LEU cc_start: 0.8378 (mt) cc_final: 0.8110 (pt) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 0.3890 time to fit residues: 46.4926 Evaluate side-chains 84 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5491 Z= 0.295 Angle : 0.621 5.849 7484 Z= 0.323 Chirality : 0.039 0.191 854 Planarity : 0.004 0.043 935 Dihedral : 7.481 58.758 1180 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.08 % Allowed : 13.40 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.90 (0.34), residues: 614 helix: 1.18 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.26 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 40 HIS 0.008 0.002 HIS A 251 PHE 0.016 0.002 PHE A 509 TYR 0.017 0.002 TYR A 215 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7357 (mtt180) cc_final: 0.7112 (ttt180) REVERT: A 182 SER cc_start: 0.9062 (t) cc_final: 0.8808 (m) REVERT: A 183 ASN cc_start: 0.8435 (m-40) cc_final: 0.7664 (t0) REVERT: A 189 ASP cc_start: 0.8754 (t0) cc_final: 0.8242 (t70) REVERT: A 215 TYR cc_start: 0.7025 (t80) cc_final: 0.6724 (t80) REVERT: A 262 GLU cc_start: 0.7777 (tt0) cc_final: 0.6903 (tp30) REVERT: A 298 GLU cc_start: 0.8481 (tt0) cc_final: 0.8215 (tm-30) REVERT: A 341 LYS cc_start: 0.7952 (mttt) cc_final: 0.7504 (mmmt) REVERT: A 431 GLU cc_start: 0.7592 (tt0) cc_final: 0.7239 (tp30) REVERT: A 453 ARG cc_start: 0.7451 (mtt90) cc_final: 0.6811 (tmm160) REVERT: A 582 GLN cc_start: 0.8053 (mt0) cc_final: 0.7515 (tp40) REVERT: A 592 LEU cc_start: 0.8376 (mt) cc_final: 0.8104 (pt) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.4273 time to fit residues: 46.5243 Evaluate side-chains 84 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 549 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5491 Z= 0.285 Angle : 0.615 5.844 7484 Z= 0.319 Chirality : 0.039 0.191 854 Planarity : 0.004 0.041 935 Dihedral : 7.241 56.469 1180 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.45 % Allowed : 13.96 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.72 (0.34), residues: 614 helix: 1.05 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.36 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 40 HIS 0.009 0.002 HIS A 251 PHE 0.012 0.002 PHE A 505 TYR 0.017 0.001 TYR A 215 ARG 0.005 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.9065 (t) cc_final: 0.8789 (m) REVERT: A 183 ASN cc_start: 0.8454 (m-40) cc_final: 0.7652 (t0) REVERT: A 189 ASP cc_start: 0.8782 (t0) cc_final: 0.8351 (t70) REVERT: A 215 TYR cc_start: 0.7076 (t80) cc_final: 0.6795 (t80) REVERT: A 262 GLU cc_start: 0.7741 (tt0) cc_final: 0.6855 (tp30) REVERT: A 298 GLU cc_start: 0.8521 (tt0) cc_final: 0.7987 (tm-30) REVERT: A 341 LYS cc_start: 0.8118 (mttt) cc_final: 0.7715 (mmmt) REVERT: A 363 MET cc_start: 0.8332 (ttm) cc_final: 0.8054 (mmm) REVERT: A 431 GLU cc_start: 0.7658 (tt0) cc_final: 0.7251 (tp30) REVERT: A 453 ARG cc_start: 0.7512 (mtt90) cc_final: 0.6840 (tmm160) REVERT: A 582 GLN cc_start: 0.8147 (mt0) cc_final: 0.7612 (tp40) REVERT: A 592 LEU cc_start: 0.8370 (mt) cc_final: 0.8111 (pt) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.4183 time to fit residues: 44.9869 Evaluate side-chains 84 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 587 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5491 Z= 0.189 Angle : 0.563 5.500 7484 Z= 0.288 Chirality : 0.037 0.197 854 Planarity : 0.004 0.037 935 Dihedral : 6.828 56.725 1180 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.70 % Allowed : 14.53 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.02 (0.35), residues: 614 helix: 1.27 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.20 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.011 0.001 HIS A 251 PHE 0.009 0.001 PHE A 509 TYR 0.013 0.001 TYR A 215 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8965 (tp) cc_final: 0.8666 (tp) REVERT: A 182 SER cc_start: 0.9048 (t) cc_final: 0.8800 (m) REVERT: A 183 ASN cc_start: 0.8477 (m-40) cc_final: 0.8148 (t0) REVERT: A 215 TYR cc_start: 0.6877 (t80) cc_final: 0.6604 (t80) REVERT: A 262 GLU cc_start: 0.7813 (tt0) cc_final: 0.7048 (tp30) REVERT: A 298 GLU cc_start: 0.8445 (tt0) cc_final: 0.8209 (tm-30) REVERT: A 309 MET cc_start: 0.8880 (mmp) cc_final: 0.8592 (mmp) REVERT: A 341 LYS cc_start: 0.8035 (mttt) cc_final: 0.7658 (mmmt) REVERT: A 350 ARG cc_start: 0.7698 (ttt90) cc_final: 0.6808 (ptp90) REVERT: A 431 GLU cc_start: 0.7664 (tt0) cc_final: 0.7252 (tp30) REVERT: A 453 ARG cc_start: 0.7504 (mtt90) cc_final: 0.6805 (tmm160) REVERT: A 582 GLN cc_start: 0.8049 (mt0) cc_final: 0.7508 (tp40) REVERT: A 592 LEU cc_start: 0.8356 (mt) cc_final: 0.8077 (pt) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.4443 time to fit residues: 46.4299 Evaluate side-chains 82 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5491 Z= 0.300 Angle : 0.609 5.943 7484 Z= 0.315 Chirality : 0.038 0.196 854 Planarity : 0.004 0.038 935 Dihedral : 6.835 56.154 1180 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.70 % Allowed : 15.66 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.77 (0.34), residues: 614 helix: 1.12 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.41 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 40 HIS 0.008 0.002 HIS A 251 PHE 0.026 0.002 PHE A 511 TYR 0.017 0.001 TYR A 215 ARG 0.005 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7911 (tt0) cc_final: 0.7687 (tp40) REVERT: A 182 SER cc_start: 0.9067 (t) cc_final: 0.8799 (m) REVERT: A 183 ASN cc_start: 0.8523 (m-40) cc_final: 0.8169 (t0) REVERT: A 215 TYR cc_start: 0.7073 (t80) cc_final: 0.6723 (t80) REVERT: A 262 GLU cc_start: 0.7743 (tt0) cc_final: 0.6844 (tp30) REVERT: A 298 GLU cc_start: 0.8497 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 341 LYS cc_start: 0.8144 (mttt) cc_final: 0.7837 (mmpt) REVERT: A 350 ARG cc_start: 0.7677 (ttt90) cc_final: 0.6792 (ptp90) REVERT: A 363 MET cc_start: 0.8329 (ttm) cc_final: 0.8076 (mmm) REVERT: A 431 GLU cc_start: 0.7658 (tt0) cc_final: 0.7260 (tp30) REVERT: A 453 ARG cc_start: 0.7436 (mtt90) cc_final: 0.6625 (tmm160) REVERT: A 582 GLN cc_start: 0.8078 (mt0) cc_final: 0.7512 (tp40) REVERT: A 592 LEU cc_start: 0.8391 (mt) cc_final: 0.8077 (pt) outliers start: 9 outliers final: 7 residues processed: 80 average time/residue: 0.4393 time to fit residues: 44.1069 Evaluate side-chains 80 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5491 Z= 0.177 Angle : 0.555 5.416 7484 Z= 0.284 Chirality : 0.036 0.204 854 Planarity : 0.004 0.036 935 Dihedral : 6.456 56.332 1180 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.51 % Allowed : 16.23 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.12 (0.35), residues: 614 helix: 1.37 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.22 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 599 HIS 0.009 0.001 HIS A 251 PHE 0.025 0.002 PHE A 511 TYR 0.012 0.001 TYR A 215 ARG 0.003 0.000 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7884 (tt0) cc_final: 0.7666 (tp40) REVERT: A 156 LEU cc_start: 0.8972 (tp) cc_final: 0.8686 (tp) REVERT: A 182 SER cc_start: 0.9037 (t) cc_final: 0.8784 (m) REVERT: A 183 ASN cc_start: 0.8523 (m-40) cc_final: 0.8175 (t0) REVERT: A 262 GLU cc_start: 0.7805 (tt0) cc_final: 0.7082 (tp30) REVERT: A 298 GLU cc_start: 0.8432 (tt0) cc_final: 0.7907 (tm-30) REVERT: A 309 MET cc_start: 0.8863 (mmp) cc_final: 0.8373 (mmp) REVERT: A 341 LYS cc_start: 0.8059 (mttt) cc_final: 0.7694 (mmmt) REVERT: A 350 ARG cc_start: 0.7640 (ttt90) cc_final: 0.6769 (ptp90) REVERT: A 363 MET cc_start: 0.8302 (ttm) cc_final: 0.7703 (tpp) REVERT: A 431 GLU cc_start: 0.7673 (tt0) cc_final: 0.7263 (tp30) REVERT: A 453 ARG cc_start: 0.7415 (mtt90) cc_final: 0.6613 (tmm160) REVERT: A 582 GLN cc_start: 0.8044 (mt0) cc_final: 0.7507 (tp40) REVERT: A 592 LEU cc_start: 0.8333 (mt) cc_final: 0.8006 (pt) outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.4340 time to fit residues: 43.0842 Evaluate side-chains 79 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5491 Z= 0.170 Angle : 0.544 5.479 7484 Z= 0.279 Chirality : 0.035 0.197 854 Planarity : 0.004 0.034 935 Dihedral : 6.157 56.205 1180 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.32 % Allowed : 16.23 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.28 (0.35), residues: 614 helix: 1.51 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 599 HIS 0.005 0.001 HIS A 251 PHE 0.020 0.001 PHE A 511 TYR 0.013 0.001 TYR A 215 ARG 0.003 0.000 ARG A 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLN cc_start: 0.7909 (tt0) cc_final: 0.7698 (tp40) REVERT: A 182 SER cc_start: 0.9002 (t) cc_final: 0.8769 (m) REVERT: A 183 ASN cc_start: 0.8543 (m-40) cc_final: 0.8202 (t0) REVERT: A 262 GLU cc_start: 0.7785 (tt0) cc_final: 0.7046 (tp30) REVERT: A 298 GLU cc_start: 0.8434 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 309 MET cc_start: 0.8835 (mmp) cc_final: 0.8354 (mmp) REVERT: A 341 LYS cc_start: 0.8038 (mttt) cc_final: 0.7680 (mmmt) REVERT: A 363 MET cc_start: 0.8291 (ttm) cc_final: 0.7682 (tpp) REVERT: A 431 GLU cc_start: 0.7656 (tt0) cc_final: 0.7256 (tp30) REVERT: A 453 ARG cc_start: 0.7438 (mtt90) cc_final: 0.6642 (tmm160) REVERT: A 582 GLN cc_start: 0.7992 (mt0) cc_final: 0.7462 (tp40) REVERT: A 592 LEU cc_start: 0.8315 (mt) cc_final: 0.7961 (pt) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.4099 time to fit residues: 40.5999 Evaluate side-chains 76 residues out of total 530 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 498 TYR Chi-restraints excluded: chain A residue 544 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091143 restraints weight = 29039.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096025 restraints weight = 11373.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099224 restraints weight = 6027.782| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 0.031 5491 Z= 0.236 Angle : 0.569 5.532 7484 Z= 0.293 Chirality : 0.036 0.187 854 Planarity : 0.004 0.038 935 Dihedral : 6.168 55.906 1180 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.32 % Allowed : 16.60 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.09 (0.35), residues: 614 helix: 1.38 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.29 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 599 HIS 0.007 0.001 HIS A 251 PHE 0.033 0.002 PHE A 509 TYR 0.014 0.001 TYR A 215 ARG 0.004 0.000 ARG A 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.55 seconds wall clock time: 52 minutes 28.08 seconds (3148.08 seconds total)