Starting phenix.real_space_refine on Sat Apr 6 12:12:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/04_2024/8u1n_41818_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/04_2024/8u1n_41818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/04_2024/8u1n_41818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/04_2024/8u1n_41818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/04_2024/8u1n_41818_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1n_41818/04_2024/8u1n_41818_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5158 2.51 5 N 1366 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8164 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4050 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain breaks: 1 Chain: "B" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4050 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 11, 'TRANS': 485} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.66, per 1000 atoms: 0.82 Number of scatterers: 8164 At special positions: 0 Unit cell: (115.83, 120.978, 103.818, 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) S 28 16.00 P 6 15.00 Mg 2 11.99 O 1604 8.00 N 1366 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 5 sheets defined 32.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 37 through 60 removed outlier: 3.650A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.647A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 66 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 67' Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 4.031A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 398 through 420 removed outlier: 3.681A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 442 removed outlier: 6.972A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.834A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 removed outlier: 4.388A pdb=" N SER A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 495 Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.987A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.899A pdb=" N VAL A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 31 removed outlier: 3.607A pdb=" N MET B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 60 removed outlier: 3.819A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 397 through 420 removed outlier: 4.287A pdb=" N GLU B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 removed outlier: 6.937A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.615A pdb=" N VAL B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 497 through 503 removed outlier: 3.952A pdb=" N ARG B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 Processing sheet with id= A, first strand: chain 'A' and resid 212 through 215 removed outlier: 3.558A pdb=" N ILE A 75 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 88 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 168 " --> pdb=" O MET A 156 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 removed outlier: 7.014A pdb=" N LYS A 353 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A 378 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 330 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 320 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 316 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 483 through 485 Processing sheet with id= D, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.956A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 143 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 159 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 168 " --> pdb=" O MET B 156 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 317 through 322 removed outlier: 3.575A pdb=" N LEU B 332 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE B 320 " --> pdb=" O ALA B 330 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 633 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: 2.06 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2661 1.34 - 1.46: 1767 1.46 - 1.58: 3826 1.58 - 1.70: 4 1.70 - 1.82: 48 Bond restraints: 8306 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.93e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.222 0.221 1.00e-02 1.00e+04 4.90e+02 bond pdb=" C1' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.416 1.359 0.057 1.30e-02 5.92e+03 1.94e+01 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.377 0.046 1.10e-02 8.26e+03 1.73e+01 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 80.15 - 95.26: 6 95.26 - 110.36: 1768 110.36 - 125.47: 9324 125.47 - 140.57: 82 140.57 - 155.68: 2 Bond angle restraints: 11182 Sorted by residual: angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.68 -34.41 1.00e+00 1.00e+00 1.18e+03 angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 154.53 -33.26 1.00e+00 1.00e+00 1.11e+03 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 82.86 32.33 1.76e+00 3.23e-01 3.37e+02 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 84.99 30.20 1.76e+00 3.23e-01 2.95e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 138.61 -29.78 2.33e+00 1.85e-01 1.64e+02 ... (remaining 11177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4300 17.84 - 35.67: 613 35.67 - 53.51: 153 53.51 - 71.34: 34 71.34 - 89.18: 16 Dihedral angle restraints: 5116 sinusoidal: 2194 harmonic: 2922 Sorted by residual: dihedral pdb=" CA TYR B 511 " pdb=" C TYR B 511 " pdb=" N MET B 512 " pdb=" CA MET B 512 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TYR A 507 " pdb=" C TYR A 507 " pdb=" N GLU A 508 " pdb=" CA GLU A 508 " ideal model delta harmonic sigma weight residual 180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLU B 514 " pdb=" C GLU B 514 " pdb=" N PRO B 515 " pdb=" CA PRO B 515 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1161 0.096 - 0.192: 55 0.192 - 0.288: 4 0.288 - 0.384: 0 0.384 - 0.480: 2 Chirality restraints: 1222 Sorted by residual: chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.95 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1219 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 514 " -0.058 5.00e-02 4.00e+02 8.71e-02 1.21e+01 pdb=" N PRO B 515 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 285 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO B 286 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 76 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 77 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.024 5.00e-02 4.00e+02 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 90 2.49 - 3.09: 5803 3.09 - 3.69: 12989 3.69 - 4.30: 17771 4.30 - 4.90: 28008 Nonbonded interactions: 64661 Sorted by model distance: nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 1.883 2.170 nonbonded pdb=" O5' ATP B 801 " pdb="MG MG B 802 " model vdw 1.893 2.170 nonbonded pdb=" O2A ATP B 801 " pdb="MG MG B 802 " model vdw 1.914 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.915 2.170 nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 1.962 2.170 ... (remaining 64656 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 'A' selection = chain 'B' } 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: 4.360 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: 3.490 Check model and map are aligned: 0.230 Set scattering table: 0.200 Process input model: 28.710 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.005 0.222 8306 Z= 0.371 Angle : 1.169 34.407 11182 Z= 0.710 Chirality : 0.048 0.480 1222 Planarity : 0.004 0.087 1426 Dihedral : 17.981 89.180 3232 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 26.00 % Favored : 74.00 % 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: -1.18 (0.26), residues: 986 helix: -0.15 (0.29), residues: 317 sheet: 0.20 (0.44), residues: 158 loop : -1.53 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 311 HIS 0.004 0.001 HIS A 481 PHE 0.010 0.001 PHE B 165 TYR 0.023 0.001 TYR B 519 ARG 0.004 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 LEU cc_start: 0.8395 (mt) cc_final: 0.8118 (mt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1699 time to fit residues: 14.5642 Evaluate side-chains 45 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.0870 chunk 46 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 overall best weight: 4.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN A 479 GLN A 492 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 8306 Z= 0.361 Angle : 0.678 8.162 11182 Z= 0.355 Chirality : 0.043 0.161 1222 Planarity : 0.005 0.059 1426 Dihedral : 10.483 76.852 1150 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.03 % Allowed : 24.33 % Favored : 69.64 % 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: -1.56 (0.26), residues: 986 helix: -0.63 (0.27), residues: 318 sheet: -0.10 (0.42), residues: 176 loop : -1.65 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 311 HIS 0.005 0.001 HIS A 481 PHE 0.015 0.002 PHE B 165 TYR 0.019 0.002 TYR A 527 ARG 0.004 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 41 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.6702 (mmt) cc_final: 0.5958 (mmt) REVERT: A 117 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 267 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.6962 (pptt) REVERT: A 278 ASP cc_start: 0.2731 (OUTLIER) cc_final: 0.2194 (m-30) REVERT: A 469 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9087 (mtmm) REVERT: A 512 MET cc_start: 0.3235 (mmp) cc_final: 0.3032 (mmp) REVERT: B 84 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6258 (t80) REVERT: B 152 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8561 (t70) REVERT: B 300 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4670 (m-10) REVERT: B 362 MET cc_start: 0.8372 (ttm) cc_final: 0.7893 (ttt) outliers start: 54 outliers final: 28 residues processed: 90 average time/residue: 0.1584 time to fit residues: 21.4814 Evaluate side-chains 74 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 39 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 8306 Z= 0.437 Angle : 0.741 8.671 11182 Z= 0.386 Chirality : 0.044 0.132 1222 Planarity : 0.005 0.055 1426 Dihedral : 10.061 78.741 1150 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 29.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 8.26 % Allowed : 23.21 % Favored : 68.53 % 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: -1.95 (0.25), residues: 986 helix: -0.95 (0.27), residues: 309 sheet: -0.44 (0.42), residues: 173 loop : -1.82 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 157 HIS 0.005 0.002 HIS A 441 PHE 0.018 0.002 PHE B 165 TYR 0.019 0.002 TYR A 428 ARG 0.005 0.001 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 38 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7270 (t0) REVERT: A 117 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 125 MET cc_start: 0.8469 (mmm) cc_final: 0.8071 (mmm) REVERT: A 138 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9375 (tp) REVERT: A 148 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8776 (tmtt) REVERT: A 278 ASP cc_start: 0.2779 (OUTLIER) cc_final: 0.2231 (m-30) REVERT: A 469 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9052 (mtmm) REVERT: A 527 TYR cc_start: 0.8238 (t80) cc_final: 0.7744 (t80) REVERT: B 84 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6382 (t80) REVERT: B 152 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8512 (t70) REVERT: B 342 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5261 (tp) REVERT: B 398 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6523 (pttm) REVERT: B 512 MET cc_start: 0.5979 (tmm) cc_final: 0.5697 (tmm) outliers start: 74 outliers final: 45 residues processed: 104 average time/residue: 0.1820 time to fit residues: 27.2683 Evaluate side-chains 88 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 33 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 411 CYS Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8306 Z= 0.232 Angle : 0.606 8.348 11182 Z= 0.319 Chirality : 0.042 0.130 1222 Planarity : 0.004 0.053 1426 Dihedral : 9.680 82.327 1150 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.36 % Allowed : 26.79 % Favored : 67.86 % 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: -1.67 (0.26), residues: 986 helix: -0.60 (0.28), residues: 296 sheet: -0.34 (0.43), residues: 173 loop : -1.69 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.003 0.001 HIS A 441 PHE 0.014 0.001 PHE B 165 TYR 0.016 0.002 TYR A 428 ARG 0.003 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 38 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8379 (mp) REVERT: A 267 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.6700 (pptt) REVERT: A 363 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8307 (p0) REVERT: A 469 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.9052 (mtmm) REVERT: A 527 TYR cc_start: 0.8161 (t80) cc_final: 0.7704 (t80) REVERT: B 93 MET cc_start: 0.7911 (mmt) cc_final: 0.7317 (mmt) REVERT: B 152 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8587 (t70) REVERT: B 362 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7929 (ttt) outliers start: 48 outliers final: 29 residues processed: 77 average time/residue: 0.1767 time to fit residues: 20.1285 Evaluate side-chains 71 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 36 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 8306 Z= 0.459 Angle : 0.773 9.167 11182 Z= 0.401 Chirality : 0.045 0.135 1222 Planarity : 0.005 0.062 1426 Dihedral : 10.155 79.861 1150 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 32.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 9.15 % Allowed : 25.89 % Favored : 64.96 % 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: -2.09 (0.26), residues: 986 helix: -1.12 (0.27), residues: 306 sheet: -0.63 (0.43), residues: 171 loop : -1.81 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 311 HIS 0.005 0.002 HIS A 441 PHE 0.020 0.002 PHE B 165 TYR 0.019 0.002 TYR A 428 ARG 0.005 0.001 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 34 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 46 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7512 (t0) REVERT: A 93 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8240 (mmt) REVERT: A 117 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 148 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8702 (tmtt) REVERT: A 363 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8300 (p0) REVERT: A 527 TYR cc_start: 0.8357 (t80) cc_final: 0.7927 (t80) REVERT: B 84 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6318 (t80) REVERT: B 152 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8500 (t70) REVERT: B 300 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.4849 (m-10) REVERT: B 342 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.5338 (tp) REVERT: B 362 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.7943 (ttt) REVERT: B 398 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6379 (pttm) REVERT: B 517 ASP cc_start: 0.7259 (m-30) cc_final: 0.6947 (m-30) outliers start: 82 outliers final: 55 residues processed: 108 average time/residue: 0.1835 time to fit residues: 28.6252 Evaluate side-chains 100 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 33 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 491 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8306 Z= 0.198 Angle : 0.599 8.741 11182 Z= 0.314 Chirality : 0.042 0.131 1222 Planarity : 0.004 0.055 1426 Dihedral : 9.472 85.712 1150 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.36 % Allowed : 29.46 % Favored : 65.18 % 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: -1.74 (0.26), residues: 986 helix: -0.65 (0.28), residues: 309 sheet: -0.50 (0.43), residues: 173 loop : -1.70 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.003 0.001 HIS B 205 PHE 0.013 0.001 PHE B 165 TYR 0.015 0.002 TYR A 428 ARG 0.002 0.000 ARG B 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 38 time to evaluate : 1.638 Fit side-chains REVERT: A 93 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6614 (mmp) REVERT: A 117 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 267 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.6624 (pptt) REVERT: A 278 ASP cc_start: 0.3081 (OUTLIER) cc_final: 0.2619 (m-30) REVERT: A 345 ASN cc_start: 0.3493 (OUTLIER) cc_final: 0.3136 (t0) REVERT: A 363 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8297 (p0) REVERT: A 527 TYR cc_start: 0.8247 (t80) cc_final: 0.7850 (t80) REVERT: B 24 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9123 (mt) REVERT: B 84 PHE cc_start: 0.7062 (OUTLIER) cc_final: 0.6214 (t80) REVERT: B 152 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8502 (t70) REVERT: B 300 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.4583 (m-10) REVERT: B 342 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5171 (tp) REVERT: B 362 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7937 (ttt) REVERT: B 517 ASP cc_start: 0.6908 (m-30) cc_final: 0.6675 (m-30) outliers start: 48 outliers final: 26 residues processed: 80 average time/residue: 0.1614 time to fit residues: 20.0743 Evaluate side-chains 77 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 39 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8306 Z= 0.234 Angle : 0.601 9.609 11182 Z= 0.313 Chirality : 0.042 0.127 1222 Planarity : 0.004 0.054 1426 Dihedral : 9.342 86.134 1150 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 6.03 % Allowed : 28.35 % Favored : 65.62 % 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: -1.67 (0.26), residues: 986 helix: -0.56 (0.28), residues: 306 sheet: -0.49 (0.43), residues: 173 loop : -1.68 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.004 0.001 HIS B 205 PHE 0.014 0.001 PHE B 165 TYR 0.015 0.002 TYR B 372 ARG 0.002 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 39 time to evaluate : 0.922 Fit side-chains REVERT: A 17 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8386 (m-80) REVERT: A 117 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 267 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6718 (pptt) REVERT: A 278 ASP cc_start: 0.3294 (OUTLIER) cc_final: 0.2772 (m-30) REVERT: A 345 ASN cc_start: 0.3337 (OUTLIER) cc_final: 0.2871 (t0) REVERT: A 363 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8303 (p0) REVERT: A 527 TYR cc_start: 0.8300 (t80) cc_final: 0.7903 (t80) REVERT: B 84 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6237 (t80) REVERT: B 152 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8530 (t70) REVERT: B 300 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.4553 (m-10) REVERT: B 342 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.5302 (tp) REVERT: B 362 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7863 (ttt) REVERT: B 398 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6570 (pttm) REVERT: B 517 ASP cc_start: 0.6996 (m-30) cc_final: 0.6759 (m-30) outliers start: 54 outliers final: 36 residues processed: 85 average time/residue: 0.1582 time to fit residues: 20.4594 Evaluate side-chains 85 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 37 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 30.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8306 Z= 0.243 Angle : 0.603 9.820 11182 Z= 0.315 Chirality : 0.042 0.130 1222 Planarity : 0.004 0.054 1426 Dihedral : 9.275 86.277 1150 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.80 % Allowed : 29.02 % Favored : 65.18 % 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: -1.56 (0.27), residues: 986 helix: -0.45 (0.29), residues: 303 sheet: -0.51 (0.43), residues: 173 loop : -1.58 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS B 205 PHE 0.014 0.001 PHE B 165 TYR 0.015 0.002 TYR A 428 ARG 0.005 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 40 time to evaluate : 0.860 Fit side-chains REVERT: A 17 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 93 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6948 (mmp) REVERT: A 117 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8381 (mp) REVERT: A 125 MET cc_start: 0.8500 (mmm) cc_final: 0.8237 (mmm) REVERT: A 267 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6654 (pptt) REVERT: A 278 ASP cc_start: 0.3209 (OUTLIER) cc_final: 0.2722 (m-30) REVERT: A 345 ASN cc_start: 0.3360 (OUTLIER) cc_final: 0.2705 (t0) REVERT: A 363 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8301 (p0) REVERT: A 527 TYR cc_start: 0.8334 (t80) cc_final: 0.7959 (t80) REVERT: B 84 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6223 (t80) REVERT: B 152 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8453 (t0) REVERT: B 300 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.4512 (m-10) REVERT: B 342 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5258 (tp) REVERT: B 362 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7865 (ttt) REVERT: B 398 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6560 (pttm) REVERT: B 441 HIS cc_start: 0.7653 (t70) cc_final: 0.6993 (t70) REVERT: B 517 ASP cc_start: 0.6955 (m-30) cc_final: 0.6723 (m-30) outliers start: 52 outliers final: 36 residues processed: 85 average time/residue: 0.1536 time to fit residues: 19.7330 Evaluate side-chains 87 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 38 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 398 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 90 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8306 Z= 0.177 Angle : 0.593 10.874 11182 Z= 0.304 Chirality : 0.041 0.164 1222 Planarity : 0.004 0.053 1426 Dihedral : 8.911 83.608 1150 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.46 % Allowed : 30.58 % Favored : 64.96 % 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: -1.41 (0.27), residues: 986 helix: -0.26 (0.30), residues: 301 sheet: -0.37 (0.43), residues: 173 loop : -1.56 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.003 0.001 HIS B 205 PHE 0.011 0.001 PHE B 165 TYR 0.013 0.001 TYR B 511 ARG 0.002 0.000 ARG B 501 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 43 time to evaluate : 0.868 Fit side-chains REVERT: A 17 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: A 117 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 125 MET cc_start: 0.8565 (mmm) cc_final: 0.8144 (mmm) REVERT: A 267 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6555 (pptt) REVERT: A 278 ASP cc_start: 0.3156 (OUTLIER) cc_final: 0.2491 (m-30) REVERT: A 345 ASN cc_start: 0.3264 (OUTLIER) cc_final: 0.2758 (t0) REVERT: A 363 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8288 (p0) REVERT: A 428 TYR cc_start: 0.9131 (t80) cc_final: 0.8926 (t80) REVERT: A 527 TYR cc_start: 0.8305 (t80) cc_final: 0.7927 (t80) REVERT: B 24 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9060 (mt) REVERT: B 84 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6142 (t80) REVERT: B 152 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8555 (t0) REVERT: B 300 TYR cc_start: 0.4763 (OUTLIER) cc_final: 0.4481 (m-10) REVERT: B 342 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5266 (tp) REVERT: B 441 HIS cc_start: 0.7768 (t70) cc_final: 0.7184 (t-170) REVERT: B 517 ASP cc_start: 0.6832 (m-30) cc_final: 0.6622 (m-30) outliers start: 40 outliers final: 24 residues processed: 78 average time/residue: 0.1515 time to fit residues: 18.4855 Evaluate side-chains 74 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 39 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8306 Z= 0.236 Angle : 0.611 11.018 11182 Z= 0.314 Chirality : 0.042 0.186 1222 Planarity : 0.004 0.053 1426 Dihedral : 9.002 84.196 1150 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.69 % Allowed : 30.47 % Favored : 64.84 % 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: -1.42 (0.27), residues: 986 helix: -0.29 (0.29), residues: 300 sheet: -0.46 (0.43), residues: 174 loop : -1.51 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.005 0.001 HIS B 205 PHE 0.013 0.001 PHE B 165 TYR 0.015 0.001 TYR B 511 ARG 0.002 0.000 ARG A 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 37 time to evaluate : 0.843 Fit side-chains REVERT: A 17 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: A 117 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8319 (mp) REVERT: A 125 MET cc_start: 0.8522 (mmm) cc_final: 0.8207 (mmm) REVERT: A 267 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6539 (pptt) REVERT: A 278 ASP cc_start: 0.3287 (OUTLIER) cc_final: 0.2580 (m-30) REVERT: A 345 ASN cc_start: 0.3432 (OUTLIER) cc_final: 0.2782 (t0) REVERT: A 363 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8311 (p0) REVERT: A 527 TYR cc_start: 0.8350 (t80) cc_final: 0.7991 (t80) REVERT: B 24 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9070 (mt) REVERT: B 84 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6172 (t80) REVERT: B 152 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8518 (t0) REVERT: B 300 TYR cc_start: 0.4796 (OUTLIER) cc_final: 0.4492 (m-10) REVERT: B 342 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5298 (tp) REVERT: B 362 MET cc_start: 0.7951 (ttt) cc_final: 0.7696 (ttt) REVERT: B 441 HIS cc_start: 0.7719 (t70) cc_final: 0.7118 (t70) REVERT: B 517 ASP cc_start: 0.6963 (m-30) cc_final: 0.6748 (m-30) outliers start: 42 outliers final: 30 residues processed: 74 average time/residue: 0.1556 time to fit residues: 17.8440 Evaluate side-chains 77 residues out of total 896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 36 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 519 TYR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 545 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.065170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.045980 restraints weight = 43887.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.047958 restraints weight = 23486.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.049185 restraints weight = 16165.912| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8306 Z= 0.228 Angle : 0.608 10.508 11182 Z= 0.312 Chirality : 0.042 0.161 1222 Planarity : 0.004 0.053 1426 Dihedral : 8.974 85.738 1150 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.80 % Allowed : 30.47 % Favored : 64.73 % 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 (0.27), residues: 986 helix: -0.21 (0.29), residues: 297 sheet: -0.42 (0.43), residues: 173 loop : -1.58 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 311 HIS 0.004 0.001 HIS B 205 PHE 0.013 0.001 PHE B 165 TYR 0.015 0.001 TYR B 511 ARG 0.002 0.000 ARG B 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.91 seconds wall clock time: 31 minutes 9.67 seconds (1869.67 seconds total)