Starting phenix.real_space_refine on Mon Mar 11 00:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/03_2024/7vq4_32085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/03_2024/7vq4_32085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/03_2024/7vq4_32085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/03_2024/7vq4_32085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/03_2024/7vq4_32085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq4_32085/03_2024/7vq4_32085.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Time building chain proxies: 3.86, per 1000 atoms: 0.61 Number of scatterers: 6306 At special positions: 0 Unit cell: (82.134, 84.162, 111.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 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: 2.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.624A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.863A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.756A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.524A pdb=" N LYS A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 187 through 214 removed outlier: 3.694A pdb=" N ASP A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.738A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.624A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.864A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.757A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.523A pdb=" N LYS B 131 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.601A pdb=" N SER B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 Processing helix chain 'B' and resid 187 through 214 removed outlier: 3.693A pdb=" N ASP B 191 " --> pdb=" O TRP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.615A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 267 through 293 removed outlier: 3.720A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.833A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.737A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN B 330 " --> pdb=" O ILE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.368A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 509 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 2.48 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: 2008 1.34 - 1.46: 1045 1.46 - 1.57: 3321 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB TRP B 57 " pdb=" CG TRP B 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP A 57 " pdb=" CG TRP A 57 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP B 187 " pdb=" CG TRP B 187 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.63e+00 bond pdb=" CB TRP A 187 " pdb=" CG TRP A 187 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.62e+00 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.14e+00 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.39: 130 106.39 - 113.28: 3643 113.28 - 120.17: 2463 120.17 - 127.06: 2400 127.06 - 133.95: 56 Bond angle restraints: 8692 Sorted by residual: angle pdb=" N VAL B 105 " pdb=" CA VAL B 105 " pdb=" C VAL B 105 " ideal model delta sigma weight residual 112.17 108.66 3.51 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N VAL A 105 " pdb=" CA VAL A 105 " pdb=" C VAL A 105 " ideal model delta sigma weight residual 112.17 108.67 3.50 9.50e-01 1.11e+00 1.36e+01 angle pdb=" N PHE B 134 " pdb=" CA PHE B 134 " pdb=" C PHE B 134 " ideal model delta sigma weight residual 110.44 114.21 -3.77 1.20e+00 6.94e-01 9.89e+00 angle pdb=" N PHE A 134 " pdb=" CA PHE A 134 " pdb=" C PHE A 134 " ideal model delta sigma weight residual 110.44 114.16 -3.72 1.20e+00 6.94e-01 9.62e+00 angle pdb=" CA PRO B 267 " pdb=" C PRO B 267 " pdb=" O PRO B 267 " ideal model delta sigma weight residual 123.07 119.36 3.71 1.38e+00 5.25e-01 7.22e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 3396 18.03 - 36.05: 366 36.05 - 54.08: 62 54.08 - 72.10: 26 72.10 - 90.13: 6 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N PRO A 185 " pdb=" CA PRO A 185 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA CYS B 184 " pdb=" C CYS B 184 " pdb=" N PRO B 185 " pdb=" CA PRO B 185 " ideal model delta harmonic sigma weight residual -180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -162.77 -17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 499 0.030 - 0.060: 357 0.060 - 0.090: 105 0.090 - 0.119: 30 0.119 - 0.149: 5 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PRO B 365 " pdb=" N PRO B 365 " pdb=" C PRO B 365 " pdb=" CB PRO B 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO A 365 " pdb=" N PRO A 365 " pdb=" C PRO A 365 " pdb=" CB PRO A 365 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO A 365 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 365 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 127 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 128 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.021 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 239 2.70 - 3.25: 6944 3.25 - 3.80: 10031 3.80 - 4.35: 11847 4.35 - 4.90: 20167 Nonbonded interactions: 49228 Sorted by model distance: nonbonded pdb=" OD1 ASP A 295 " pdb=" N PHE A 296 " model vdw 2.155 2.520 nonbonded pdb=" OD1 ASP B 295 " pdb=" N PHE B 296 " model vdw 2.155 2.520 nonbonded pdb=" O MET B 1 " pdb=" N ARG B 5 " model vdw 2.178 2.520 nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.209 2.440 nonbonded pdb=" NH1 ARG A 80 " pdb=" OH TYR A 136 " model vdw 2.225 2.520 ... (remaining 49223 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 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: 1.590 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.090 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 6434 Z= 0.439 Angle : 0.740 7.518 8692 Z= 0.423 Chirality : 0.042 0.149 996 Planarity : 0.004 0.050 1090 Dihedral : 16.105 90.127 2352 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.30 % Allowed : 8.62 % Favored : 89.08 % 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: -1.96 (0.27), residues: 792 helix: -0.72 (0.18), residues: 666 sheet: None (None), residues: 0 loop : -3.76 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 266 PHE 0.018 0.002 PHE B 153 TYR 0.013 0.002 TYR B 291 ARG 0.003 0.001 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 0.696 Fit side-chains REVERT: A 40 TYR cc_start: 0.8043 (t80) cc_final: 0.7503 (t80) REVERT: A 180 SER cc_start: 0.9003 (t) cc_final: 0.8580 (p) REVERT: A 237 LYS cc_start: 0.8450 (mttt) cc_final: 0.8150 (mtmt) REVERT: A 306 LEU cc_start: 0.8688 (tp) cc_final: 0.8481 (tp) REVERT: A 307 GLU cc_start: 0.7515 (pt0) cc_final: 0.7258 (pm20) REVERT: A 322 LYS cc_start: 0.7820 (tptm) cc_final: 0.7412 (ttpt) REVERT: B 1 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4477 (ptp) REVERT: B 40 TYR cc_start: 0.8064 (t80) cc_final: 0.7540 (t80) REVERT: B 328 LEU cc_start: 0.9183 (tp) cc_final: 0.8902 (tp) outliers start: 16 outliers final: 7 residues processed: 216 average time/residue: 0.2248 time to fit residues: 60.3787 Evaluate side-chains 162 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 223 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 54 ASN A 79 ASN A 251 ASN A 259 HIS A 293 ASN A 297 GLN A 340 HIS A 343 ASN B 24 HIS B 54 ASN B 79 ASN B 251 ASN B 259 HIS B 280 GLN B 293 ASN B 297 GLN B 330 GLN B 340 HIS B 343 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6434 Z= 0.194 Angle : 0.542 5.808 8692 Z= 0.286 Chirality : 0.037 0.146 996 Planarity : 0.004 0.046 1090 Dihedral : 5.561 54.998 870 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.60 % Allowed : 16.95 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 792 helix: 1.61 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -3.23 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 57 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE A 145 TYR 0.014 0.001 TYR A 291 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7654 (tmm160) cc_final: 0.7423 (tmt170) REVERT: A 105 VAL cc_start: 0.6377 (OUTLIER) cc_final: 0.6039 (t) REVERT: A 180 SER cc_start: 0.8854 (t) cc_final: 0.8459 (p) REVERT: A 193 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6729 (t-90) REVERT: A 263 ARG cc_start: 0.7819 (tpp80) cc_final: 0.7252 (tmt170) REVERT: A 322 LYS cc_start: 0.7651 (tptm) cc_final: 0.7070 (ttpt) REVERT: A 368 MET cc_start: 0.7704 (mmm) cc_final: 0.7488 (mmm) REVERT: B 1 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.4893 (tpp) REVERT: B 9 ARG cc_start: 0.6614 (mtt-85) cc_final: 0.5904 (ptp90) REVERT: B 193 HIS cc_start: 0.7186 (OUTLIER) cc_final: 0.6891 (t-90) REVERT: B 237 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7953 (mtmt) REVERT: B 328 LEU cc_start: 0.9026 (tp) cc_final: 0.8599 (tp) outliers start: 32 outliers final: 19 residues processed: 187 average time/residue: 0.1938 time to fit residues: 46.8559 Evaluate side-chains 175 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN B 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6434 Z= 0.195 Angle : 0.530 5.934 8692 Z= 0.276 Chirality : 0.037 0.161 996 Planarity : 0.004 0.049 1090 Dihedral : 4.898 53.174 869 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.89 % Allowed : 18.25 % Favored : 75.86 % 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: 2.15 (0.31), residues: 792 helix: 2.20 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.84 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.004 0.001 HIS B 95 PHE 0.012 0.001 PHE B 141 TYR 0.011 0.001 TYR B 236 ARG 0.006 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.6468 (OUTLIER) cc_final: 0.6191 (t) REVERT: A 180 SER cc_start: 0.8917 (t) cc_final: 0.8493 (p) REVERT: A 193 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6834 (t-90) REVERT: A 322 LYS cc_start: 0.7552 (tptm) cc_final: 0.6871 (ttpt) REVERT: B 193 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.6905 (t-90) REVERT: B 237 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8127 (mtmt) REVERT: B 265 ARG cc_start: 0.7574 (mmm-85) cc_final: 0.7287 (mtp-110) REVERT: B 328 LEU cc_start: 0.9040 (tp) cc_final: 0.8594 (tp) outliers start: 41 outliers final: 25 residues processed: 178 average time/residue: 0.1881 time to fit residues: 43.6436 Evaluate side-chains 169 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.0470 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6434 Z= 0.172 Angle : 0.522 7.117 8692 Z= 0.270 Chirality : 0.037 0.210 996 Planarity : 0.003 0.049 1090 Dihedral : 4.171 24.173 866 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.60 % Allowed : 19.83 % Favored : 74.57 % 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: 2.75 (0.31), residues: 792 helix: 2.55 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.25 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.012 0.001 PHE B 141 TYR 0.012 0.001 TYR A 236 ARG 0.005 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 HIS cc_start: 0.7216 (OUTLIER) cc_final: 0.6729 (t-90) REVERT: A 322 LYS cc_start: 0.7466 (tptm) cc_final: 0.6751 (ttpt) REVERT: B 95 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7191 (t70) REVERT: B 106 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6267 (tt0) REVERT: B 193 HIS cc_start: 0.7195 (OUTLIER) cc_final: 0.6692 (t-90) REVERT: B 237 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8134 (mtmt) REVERT: B 323 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 328 LEU cc_start: 0.8941 (tp) cc_final: 0.8518 (tp) outliers start: 39 outliers final: 25 residues processed: 175 average time/residue: 0.1855 time to fit residues: 42.0216 Evaluate side-chains 170 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 53 optimal weight: 0.0980 chunk 0 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 79 ASN B 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6434 Z= 0.163 Angle : 0.541 10.906 8692 Z= 0.273 Chirality : 0.037 0.196 996 Planarity : 0.003 0.048 1090 Dihedral : 3.970 21.602 864 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.17 % Allowed : 20.69 % Favored : 74.14 % 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: 2.97 (0.31), residues: 792 helix: 2.68 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.05 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.011 0.001 PHE B 141 TYR 0.012 0.001 TYR B 236 ARG 0.007 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.7467 (tptm) cc_final: 0.6646 (ttpt) REVERT: A 331 MET cc_start: 0.8202 (tpp) cc_final: 0.7959 (tpp) REVERT: B 1 MET cc_start: 0.5538 (ttt) cc_final: 0.5138 (tpp) REVERT: B 95 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.7037 (t70) REVERT: B 193 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6622 (t-90) REVERT: B 307 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: B 328 LEU cc_start: 0.8908 (tp) cc_final: 0.8533 (tp) outliers start: 36 outliers final: 27 residues processed: 166 average time/residue: 0.1777 time to fit residues: 39.1748 Evaluate side-chains 172 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6434 Z= 0.159 Angle : 0.555 9.640 8692 Z= 0.273 Chirality : 0.036 0.200 996 Planarity : 0.003 0.049 1090 Dihedral : 3.870 22.479 862 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.31 % Allowed : 22.84 % Favored : 72.84 % 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: 3.12 (0.31), residues: 792 helix: 2.77 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.88 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE B 145 TYR 0.012 0.001 TYR B 236 ARG 0.006 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.7463 (tptm) cc_final: 0.6677 (ttpt) REVERT: A 331 MET cc_start: 0.8214 (tpp) cc_final: 0.7953 (tpp) REVERT: B 1 MET cc_start: 0.5445 (ttt) cc_final: 0.5072 (tpp) REVERT: B 9 ARG cc_start: 0.6065 (mtt-85) cc_final: 0.5730 (ptp90) REVERT: B 95 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7024 (t70) REVERT: B 193 HIS cc_start: 0.7207 (OUTLIER) cc_final: 0.6609 (t-90) REVERT: B 283 TYR cc_start: 0.7848 (m-10) cc_final: 0.7631 (m-10) outliers start: 30 outliers final: 24 residues processed: 167 average time/residue: 0.1828 time to fit residues: 40.4466 Evaluate side-chains 162 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6434 Z= 0.168 Angle : 0.572 14.246 8692 Z= 0.279 Chirality : 0.037 0.203 996 Planarity : 0.003 0.048 1090 Dihedral : 3.876 22.601 862 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.31 % Allowed : 24.28 % Favored : 71.41 % 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: 3.17 (0.31), residues: 792 helix: 2.78 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.73 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.009 0.001 PHE B 141 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.7466 (tptm) cc_final: 0.6656 (ttpt) REVERT: A 372 MET cc_start: 0.8276 (mmt) cc_final: 0.8027 (mmt) REVERT: A 405 MET cc_start: 0.1934 (mpp) cc_final: 0.1408 (mmp) REVERT: B 1 MET cc_start: 0.5570 (ttt) cc_final: 0.5364 (tpp) REVERT: B 9 ARG cc_start: 0.5967 (mtt-85) cc_final: 0.5675 (ptp90) REVERT: B 95 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.7026 (t70) REVERT: B 193 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6883 (t-90) outliers start: 30 outliers final: 24 residues processed: 160 average time/residue: 0.1618 time to fit residues: 34.9783 Evaluate side-chains 162 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 193 HIS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS A 330 GLN B 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6434 Z= 0.196 Angle : 0.605 14.676 8692 Z= 0.292 Chirality : 0.037 0.204 996 Planarity : 0.004 0.048 1090 Dihedral : 3.951 22.255 862 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.45 % Allowed : 24.71 % Favored : 70.83 % 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: 3.06 (0.31), residues: 792 helix: 2.66 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.73 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 255 HIS 0.003 0.001 HIS A 259 PHE 0.028 0.001 PHE B 123 TYR 0.013 0.001 TYR B 236 ARG 0.006 0.000 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7027 (t-90) REVERT: A 321 MET cc_start: 0.7595 (mmp) cc_final: 0.7371 (mmt) REVERT: A 322 LYS cc_start: 0.7497 (tptm) cc_final: 0.6723 (ttpt) REVERT: A 331 MET cc_start: 0.8165 (tpp) cc_final: 0.7899 (tpp) REVERT: A 405 MET cc_start: 0.1942 (mpp) cc_final: 0.1256 (mmp) REVERT: B 1 MET cc_start: 0.5843 (ttt) cc_final: 0.5444 (tpp) REVERT: B 95 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7264 (t70) outliers start: 31 outliers final: 26 residues processed: 154 average time/residue: 0.1728 time to fit residues: 35.4924 Evaluate side-chains 159 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6434 Z= 0.220 Angle : 0.626 14.733 8692 Z= 0.305 Chirality : 0.038 0.204 996 Planarity : 0.004 0.046 1090 Dihedral : 4.039 23.021 862 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.60 % Allowed : 24.86 % Favored : 70.55 % 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: 3.01 (0.31), residues: 792 helix: 2.63 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.74 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.004 0.001 HIS B 259 PHE 0.011 0.001 PHE A 206 TYR 0.013 0.001 TYR B 236 ARG 0.005 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ILE cc_start: 0.7533 (pp) cc_final: 0.7172 (pp) REVERT: A 79 ASN cc_start: 0.8238 (m110) cc_final: 0.7922 (m-40) REVERT: A 321 MET cc_start: 0.7645 (mmp) cc_final: 0.7358 (mmt) REVERT: A 322 LYS cc_start: 0.7499 (tptm) cc_final: 0.6745 (ttpt) REVERT: A 331 MET cc_start: 0.8231 (tpp) cc_final: 0.7938 (tpp) REVERT: A 372 MET cc_start: 0.8280 (mmt) cc_final: 0.8064 (mmt) REVERT: A 377 MET cc_start: 0.8229 (mmt) cc_final: 0.8003 (mmm) REVERT: A 405 MET cc_start: 0.1974 (mpp) cc_final: 0.1310 (mmp) REVERT: B 1 MET cc_start: 0.6121 (ttt) cc_final: 0.5672 (tpp) REVERT: B 95 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7369 (t70) outliers start: 32 outliers final: 29 residues processed: 154 average time/residue: 0.1642 time to fit residues: 33.9002 Evaluate side-chains 162 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6434 Z= 0.248 Angle : 0.672 14.502 8692 Z= 0.326 Chirality : 0.039 0.206 996 Planarity : 0.004 0.047 1090 Dihedral : 4.158 23.424 862 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.45 % Allowed : 25.29 % Favored : 70.26 % 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: 2.82 (0.31), residues: 792 helix: 2.50 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.82 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.004 0.001 HIS A 259 PHE 0.018 0.001 PHE B 145 TYR 0.013 0.001 TYR B 236 ARG 0.007 0.001 ARG B 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7798 (ppp) cc_final: 0.7412 (ppp) REVERT: A 53 ILE cc_start: 0.7661 (pp) cc_final: 0.7300 (pp) REVERT: A 95 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7063 (t-90) REVERT: A 321 MET cc_start: 0.7678 (mmp) cc_final: 0.7428 (mmt) REVERT: A 322 LYS cc_start: 0.7519 (tptm) cc_final: 0.6762 (ttpt) REVERT: A 405 MET cc_start: 0.1367 (mpp) cc_final: 0.0840 (mmp) REVERT: B 1 MET cc_start: 0.6256 (ttt) cc_final: 0.5684 (tpp) REVERT: B 95 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7429 (t70) outliers start: 31 outliers final: 27 residues processed: 159 average time/residue: 0.1659 time to fit residues: 35.3490 Evaluate side-chains 163 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 223 TYR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 401 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** B 345 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 = 0.4010 r_free = 0.4010 target = 0.156189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129427 restraints weight = 9428.179| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.51 r_work: 0.3614 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6434 Z= 0.187 Angle : 0.636 14.849 8692 Z= 0.305 Chirality : 0.037 0.201 996 Planarity : 0.004 0.044 1090 Dihedral : 4.074 26.365 862 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.88 % Allowed : 25.72 % Favored : 70.40 % 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: 3.15 (0.31), residues: 792 helix: 2.75 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.75 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.005 0.001 HIS A 193 PHE 0.010 0.001 PHE B 141 TYR 0.014 0.001 TYR B 236 ARG 0.007 0.001 ARG B 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1564.69 seconds wall clock time: 29 minutes 15.41 seconds (1755.41 seconds total)