Starting phenix.real_space_refine on Mon Mar 11 00:21:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq3_32084/03_2024/7vq3_32084.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq3_32084/03_2024/7vq3_32084.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/7vq3_32084/03_2024/7vq3_32084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq3_32084/03_2024/7vq3_32084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq3_32084/03_2024/7vq3_32084.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq3_32084/03_2024/7vq3_32084.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 ARG 20": "NH1" <-> "NH2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 364": "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: 4.04, per 1000 atoms: 0.64 Number of scatterers: 6306 At special positions: 0 Unit cell: (84.162, 84.162, 109.512, 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: 2.47 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 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.531A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.709A 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: 3.854A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.749A 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 Processing helix chain 'A' and resid 134 through 151 Processing helix chain 'A' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.531A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.709A 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: 3.854A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.749A 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 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 515 hydrogen bonds defined for protein. 1545 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: 1.86 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2010 1.34 - 1.46: 1360 1.46 - 1.58: 3004 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB THR B 168 " pdb=" CG2 THR B 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB MET A 377 " pdb=" CG MET A 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB MET B 377 " pdb=" CG MET B 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB THR B 73 " pdb=" CG2 THR B 73 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.82e-01 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.52: 142 106.52 - 113.38: 3620 113.38 - 120.23: 2506 120.23 - 127.09: 2362 127.09 - 133.94: 62 Bond angle restraints: 8692 Sorted by residual: angle pdb=" C VAL A 105 " pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" C VAL B 105 " pdb=" N GLU B 106 " pdb=" CA GLU B 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" N GLU A 307 " pdb=" CA GLU A 307 " pdb=" C GLU A 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" N GLU B 307 " pdb=" CA GLU B 307 " pdb=" C GLU B 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" C PHE B 182 " pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 121.97 119.01 2.96 1.80e+00 3.09e-01 2.70e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 3366 16.81 - 33.61: 404 33.61 - 50.42: 74 50.42 - 67.23: 2 67.23 - 84.03: 10 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: 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 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA HIS A 259 " pdb=" C HIS A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB GLU B 307 " pdb=" CG GLU B 307 " pdb=" CD GLU B 307 " pdb=" OE1 GLU B 307 " ideal model delta sinusoidal sigma weight residual 0.00 84.03 -84.03 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.054: 346 0.054 - 0.081: 98 0.081 - 0.108: 20 0.108 - 0.135: 16 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA THR A 308 " pdb=" N THR A 308 " pdb=" C THR A 308 " pdb=" CB THR A 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA THR B 308 " pdb=" N THR B 308 " pdb=" C THR B 308 " pdb=" CB THR B 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 298 " pdb=" N ILE A 298 " pdb=" C ILE A 298 " pdb=" CB ILE A 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 365 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 365 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 257 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 42 2.63 - 3.20: 5928 3.20 - 3.76: 9359 3.76 - 4.33: 12910 4.33 - 4.90: 21301 Nonbonded interactions: 49540 Sorted by model distance: nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.061 2.440 nonbonded pdb=" OG SER A 376 " pdb=" OH TYR B 291 " model vdw 2.061 2.440 nonbonded pdb=" OE1 GLU B 213 " pdb=" ND2 ASN B 232 " model vdw 2.284 2.520 nonbonded pdb=" OE1 GLU A 213 " pdb=" ND2 ASN A 232 " model vdw 2.284 2.520 nonbonded pdb=" O SER A 294 " pdb=" NE2 GLN A 297 " model vdw 2.316 2.520 ... (remaining 49535 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: 0.250 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: 0.020 Extract box with map and model: 1.630 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.560 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 0.053 6434 Z= 0.332 Angle : 0.550 5.673 8692 Z= 0.316 Chirality : 0.039 0.135 996 Planarity : 0.004 0.037 1090 Dihedral : 14.665 84.030 2352 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 792 helix: 0.06 (0.18), residues: 642 sheet: None (None), residues: 0 loop : -3.31 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE A 200 TYR 0.012 0.001 TYR B 291 ARG 0.002 0.000 ARG B 9 *********************** 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 126 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.673 Fit side-chains REVERT: A 50 TYR cc_start: 0.7738 (t80) cc_final: 0.7338 (t80) REVERT: A 229 ARG cc_start: 0.6960 (mmt90) cc_final: 0.6567 (ttp80) REVERT: A 261 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7021 (tt0) REVERT: A 387 LYS cc_start: 0.7991 (mttt) cc_final: 0.7667 (mptt) REVERT: B 229 ARG cc_start: 0.6964 (mmt90) cc_final: 0.6578 (ttp80) REVERT: B 261 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7002 (tt0) REVERT: B 387 LYS cc_start: 0.8007 (mttt) cc_final: 0.7690 (mptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2360 time to fit residues: 37.8100 Evaluate side-chains 92 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 205 HIS A 251 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 361 ASN B 54 ASN B 96 GLN B 205 HIS B 251 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 361 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6434 Z= 0.173 Angle : 0.493 5.853 8692 Z= 0.261 Chirality : 0.038 0.129 996 Planarity : 0.004 0.043 1090 Dihedral : 3.958 18.625 858 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.44 % Allowed : 10.06 % Favored : 88.51 % 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: 1.52 (0.31), residues: 792 helix: 1.79 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.60 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.002 0.001 HIS A 259 PHE 0.012 0.001 PHE A 206 TYR 0.013 0.001 TYR A 236 ARG 0.004 0.000 ARG A 312 *********************** 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 119 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.759 Fit side-chains REVERT: A 194 SER cc_start: 0.8582 (t) cc_final: 0.8149 (m) REVERT: A 229 ARG cc_start: 0.7040 (mmt90) cc_final: 0.6746 (ttp80) REVERT: A 230 LYS cc_start: 0.8495 (tptt) cc_final: 0.8024 (tttt) REVERT: A 261 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7085 (tt0) REVERT: A 297 GLN cc_start: 0.7956 (mm110) cc_final: 0.7728 (mm110) REVERT: A 387 LYS cc_start: 0.7836 (mttt) cc_final: 0.7560 (mptt) REVERT: B 194 SER cc_start: 0.8581 (t) cc_final: 0.8128 (m) REVERT: B 229 ARG cc_start: 0.7040 (mmt90) cc_final: 0.6688 (ttp80) REVERT: B 230 LYS cc_start: 0.8498 (tptt) cc_final: 0.8040 (tttt) REVERT: B 261 GLN cc_start: 0.7833 (tp-100) cc_final: 0.7069 (tt0) REVERT: B 297 GLN cc_start: 0.7968 (mm110) cc_final: 0.7735 (mm110) REVERT: B 387 LYS cc_start: 0.7880 (mttt) cc_final: 0.7617 (mptt) outliers start: 10 outliers final: 6 residues processed: 113 average time/residue: 0.2225 time to fit residues: 32.0512 Evaluate side-chains 95 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 285 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 0.0870 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6434 Z= 0.297 Angle : 0.543 6.005 8692 Z= 0.287 Chirality : 0.039 0.132 996 Planarity : 0.004 0.046 1090 Dihedral : 3.999 19.801 858 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.30 % Allowed : 12.07 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.31), residues: 792 helix: 2.02 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -3.01 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 129 HIS 0.002 0.001 HIS B 259 PHE 0.018 0.002 PHE B 206 TYR 0.012 0.001 TYR B 271 ARG 0.001 0.000 ARG B 312 *********************** 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 112 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.780 Fit side-chains REVERT: A 229 ARG cc_start: 0.7022 (mmt90) cc_final: 0.6742 (ttp80) REVERT: A 324 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7582 (mtt) REVERT: A 387 LYS cc_start: 0.7865 (mttt) cc_final: 0.7546 (mptt) REVERT: B 229 ARG cc_start: 0.7032 (mmt90) cc_final: 0.6767 (ttp80) REVERT: B 324 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7568 (mtt) REVERT: B 387 LYS cc_start: 0.7879 (mttt) cc_final: 0.7565 (mptt) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.2079 time to fit residues: 28.0257 Evaluate side-chains 99 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2143 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= 0.177 Angle : 0.483 6.285 8692 Z= 0.256 Chirality : 0.037 0.129 996 Planarity : 0.004 0.047 1090 Dihedral : 3.810 17.954 858 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.73 % Allowed : 14.51 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.31), residues: 792 helix: 2.43 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.91 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 129 HIS 0.003 0.001 HIS A 259 PHE 0.014 0.001 PHE B 206 TYR 0.010 0.001 TYR B 39 ARG 0.002 0.000 ARG A 312 *********************** 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 115 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.750 Fit side-chains REVERT: A 229 ARG cc_start: 0.7062 (mmt90) cc_final: 0.6726 (ttp80) REVERT: A 230 LYS cc_start: 0.8420 (tptt) cc_final: 0.8021 (tptt) REVERT: A 261 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7203 (tt0) REVERT: A 387 LYS cc_start: 0.7839 (mttt) cc_final: 0.7549 (mptt) REVERT: B 230 LYS cc_start: 0.8430 (tptt) cc_final: 0.8013 (tptt) REVERT: B 261 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7184 (tt0) REVERT: B 387 LYS cc_start: 0.7828 (mttt) cc_final: 0.7562 (mptt) outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 0.2203 time to fit residues: 29.3239 Evaluate side-chains 99 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.188 Angle : 0.501 7.452 8692 Z= 0.258 Chirality : 0.037 0.136 996 Planarity : 0.004 0.046 1090 Dihedral : 3.753 16.882 858 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.73 % Allowed : 15.80 % Favored : 81.47 % 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: 2.63 (0.31), residues: 792 helix: 2.58 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.74 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.015 0.001 PHE B 206 TYR 0.021 0.001 TYR A 236 ARG 0.002 0.000 ARG A 312 *********************** 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 109 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.685 Fit side-chains REVERT: A 230 LYS cc_start: 0.8481 (tptt) cc_final: 0.8098 (tptt) REVERT: A 261 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7245 (tt0) REVERT: A 387 LYS cc_start: 0.7850 (mttt) cc_final: 0.7551 (mptt) REVERT: B 229 ARG cc_start: 0.7239 (mmt180) cc_final: 0.6767 (mtm110) REVERT: B 230 LYS cc_start: 0.8473 (tptt) cc_final: 0.8098 (tptt) REVERT: B 261 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7232 (tt0) REVERT: B 387 LYS cc_start: 0.7845 (mttt) cc_final: 0.7565 (mptt) outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.2032 time to fit residues: 26.3766 Evaluate side-chains 97 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6434 Z= 0.170 Angle : 0.488 7.394 8692 Z= 0.250 Chirality : 0.037 0.126 996 Planarity : 0.004 0.046 1090 Dihedral : 3.719 16.720 858 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.59 % Allowed : 16.09 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.31), residues: 792 helix: 2.74 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.57 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 57 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE B 206 TYR 0.021 0.001 TYR A 236 ARG 0.001 0.000 ARG B 265 *********************** 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 116 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.8497 (tptt) cc_final: 0.8157 (tptt) REVERT: A 261 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7380 (tt0) REVERT: A 387 LYS cc_start: 0.7846 (mttt) cc_final: 0.7543 (mptt) REVERT: B 229 ARG cc_start: 0.7247 (mmt180) cc_final: 0.6778 (mtm110) REVERT: B 230 LYS cc_start: 0.8475 (tptt) cc_final: 0.8167 (tptt) REVERT: B 261 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7367 (tt0) REVERT: B 387 LYS cc_start: 0.7866 (mttt) cc_final: 0.7562 (mptt) outliers start: 25 outliers final: 21 residues processed: 105 average time/residue: 0.1981 time to fit residues: 27.2316 Evaluate side-chains 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN B 117 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6434 Z= 0.290 Angle : 0.552 7.428 8692 Z= 0.285 Chirality : 0.039 0.130 996 Planarity : 0.004 0.047 1090 Dihedral : 3.869 17.492 858 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.31 % Allowed : 16.67 % Favored : 79.02 % 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: 2.60 (0.31), residues: 792 helix: 2.55 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.66 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 255 HIS 0.002 0.001 HIS A 259 PHE 0.016 0.001 PHE B 206 TYR 0.021 0.002 TYR B 236 ARG 0.001 0.000 ARG A 284 *********************** 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 125 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.752 Fit side-chains REVERT: A 230 LYS cc_start: 0.8549 (tptt) cc_final: 0.8149 (tttt) REVERT: A 261 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7252 (tt0) REVERT: A 387 LYS cc_start: 0.7868 (mttt) cc_final: 0.7529 (mptt) REVERT: B 230 LYS cc_start: 0.8536 (tptt) cc_final: 0.8146 (tttt) REVERT: B 261 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7234 (tt0) REVERT: B 387 LYS cc_start: 0.7899 (mttt) cc_final: 0.7551 (mptt) outliers start: 30 outliers final: 20 residues processed: 112 average time/residue: 0.1783 time to fit residues: 26.6717 Evaluate side-chains 106 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.177 Angle : 0.502 8.136 8692 Z= 0.258 Chirality : 0.037 0.125 996 Planarity : 0.004 0.047 1090 Dihedral : 3.739 17.454 858 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.02 % Allowed : 17.24 % Favored : 79.74 % 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: 2.96 (0.31), residues: 792 helix: 2.82 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.66 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.015 0.001 PHE B 206 TYR 0.024 0.002 TYR B 236 ARG 0.001 0.000 ARG A 265 *********************** 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 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.751 Fit side-chains REVERT: A 230 LYS cc_start: 0.8485 (tptt) cc_final: 0.8095 (tttm) REVERT: A 261 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7289 (tt0) REVERT: A 387 LYS cc_start: 0.7837 (mttt) cc_final: 0.7541 (mptt) REVERT: B 230 LYS cc_start: 0.8471 (tptt) cc_final: 0.8098 (tttm) REVERT: B 261 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7270 (tt0) REVERT: B 387 LYS cc_start: 0.7853 (mttt) cc_final: 0.7562 (mptt) outliers start: 21 outliers final: 21 residues processed: 100 average time/residue: 0.2095 time to fit residues: 27.3754 Evaluate side-chains 105 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6434 Z= 0.161 Angle : 0.490 8.188 8692 Z= 0.252 Chirality : 0.037 0.134 996 Planarity : 0.004 0.047 1090 Dihedral : 3.644 15.733 858 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.16 % Allowed : 18.25 % Favored : 78.59 % 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: 3.10 (0.31), residues: 792 helix: 2.91 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.60 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.014 0.001 PHE B 206 TYR 0.022 0.001 TYR B 236 ARG 0.001 0.000 ARG A 312 *********************** 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 112 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.777 Fit side-chains REVERT: A 230 LYS cc_start: 0.8479 (tptt) cc_final: 0.8189 (tttt) REVERT: A 261 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7406 (tt0) REVERT: A 387 LYS cc_start: 0.7877 (mttt) cc_final: 0.7554 (mptt) REVERT: B 230 LYS cc_start: 0.8472 (tptt) cc_final: 0.8198 (tttt) REVERT: B 261 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7404 (tt0) REVERT: B 387 LYS cc_start: 0.7861 (mttt) cc_final: 0.7582 (mptt) outliers start: 22 outliers final: 21 residues processed: 105 average time/residue: 0.2133 time to fit residues: 28.8075 Evaluate side-chains 106 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 0.030 6434 Z= 0.211 Angle : 0.523 8.325 8692 Z= 0.267 Chirality : 0.038 0.133 996 Planarity : 0.004 0.047 1090 Dihedral : 3.742 17.235 858 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.02 % Allowed : 18.97 % Favored : 78.02 % 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: 2.81 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.60 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.004 0.001 HIS B 259 PHE 0.015 0.001 PHE B 206 TYR 0.023 0.001 TYR B 236 ARG 0.006 0.000 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 105 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.726 Fit side-chains REVERT: A 230 LYS cc_start: 0.8480 (tptt) cc_final: 0.8164 (tttt) REVERT: A 261 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7410 (tt0) REVERT: A 324 MET cc_start: 0.7615 (ttm) cc_final: 0.7281 (ttm) REVERT: A 387 LYS cc_start: 0.7862 (mttt) cc_final: 0.7551 (mptt) REVERT: B 230 LYS cc_start: 0.8470 (tptt) cc_final: 0.8169 (tttt) REVERT: B 261 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7378 (tt0) REVERT: B 324 MET cc_start: 0.7614 (ttm) cc_final: 0.7277 (ttm) REVERT: B 387 LYS cc_start: 0.7860 (mttt) cc_final: 0.7560 (mptt) outliers start: 21 outliers final: 20 residues processed: 100 average time/residue: 0.1896 time to fit residues: 25.0677 Evaluate side-chains 99 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 363 VAL 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: 3.9990 chunk 17 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 HIS ** B 289 ASN ** 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 = 0.3871 r_free = 0.3871 target = 0.164001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122737 restraints weight = 7378.710| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.07 r_work: 0.3298 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6434 Z= 0.156 Angle : 0.491 8.363 8692 Z= 0.250 Chirality : 0.037 0.129 996 Planarity : 0.004 0.047 1090 Dihedral : 3.606 15.626 858 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.02 % Allowed : 19.11 % Favored : 77.87 % 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: 2.95 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.55 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.015 0.001 PHE B 206 TYR 0.021 0.001 TYR B 236 ARG 0.006 0.000 ARG B 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.84 seconds wall clock time: 28 minutes 23.93 seconds (1703.93 seconds total)