Starting phenix.real_space_refine on Sun Mar 10 15:34:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwj_27756/03_2024/8dwj_27756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwj_27756/03_2024/8dwj_27756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwj_27756/03_2024/8dwj_27756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwj_27756/03_2024/8dwj_27756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwj_27756/03_2024/8dwj_27756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwj_27756/03_2024/8dwj_27756_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 S 13 5.16 5 C 1905 2.51 5 N 525 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3043 Number of models: 1 Model: "" Number of chains: 3 Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNA': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2782 Unusual residues: {' ZN': 1} Classifications: {'peptide': 339, 'undetermined': 1} Link IDs: {'PTRANS': 24, 'TRANS': 314, None: 1} Not linked: pdbres="LYS A 341 " pdbres=" ZN A 401 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 556 SG CYS A 37 35.483 27.676 19.865 1.00234.26 S ATOM 576 SG CYS A 40 35.253 23.162 19.878 1.00251.45 S ATOM 775 SG CYS A 65 36.508 25.850 23.034 1.00220.03 S ATOM 801 SG CYS A 68 38.485 25.430 20.056 1.00211.90 S Time building chain proxies: 2.57, per 1000 atoms: 0.84 Number of scatterers: 3043 At special positions: 0 Unit cell: (67.914, 67.914, 82.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 13 16.00 P 14 15.00 O 585 8.00 N 525 7.00 C 1905 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 536.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 37 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 65 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 68 " Number of angles added : 6 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 3 sheets defined 33.0% alpha, 13.0% beta 3 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 83 through 96 removed outlier: 3.545A pdb=" N ARG A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 147 through 152 removed outlier: 4.212A pdb=" N LYS A 151 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.789A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 330 through 340 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 124 through 126 Processing sheet with id= C, first strand: chain 'A' and resid 264 through 266 removed outlier: 6.528A pdb=" N VAL A 230 " --> pdb=" O VAL A 265 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 1.45 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: 801 1.34 - 1.45: 621 1.45 - 1.57: 1675 1.57 - 1.69: 25 1.69 - 1.81: 20 Bond restraints: 3142 Sorted by residual: bond pdb=" N VAL A 232 " pdb=" CA VAL A 232 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.21e-02 6.83e+03 8.34e+00 bond pdb=" N ILE A 308 " pdb=" CA ILE A 308 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 8.01e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.83e+00 bond pdb=" N ILE A 103 " pdb=" CA ILE A 103 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.56e+00 bond pdb=" N SER A 100 " pdb=" CA SER A 100 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.40e+00 ... (remaining 3137 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.31: 173 106.31 - 113.29: 1625 113.29 - 120.27: 1225 120.27 - 127.24: 1212 127.24 - 134.22: 62 Bond angle restraints: 4297 Sorted by residual: angle pdb=" N ARG A 87 " pdb=" CA ARG A 87 " pdb=" C ARG A 87 " ideal model delta sigma weight residual 110.97 105.46 5.51 1.09e+00 8.42e-01 2.55e+01 angle pdb=" CA LYS A 161 " pdb=" CB LYS A 161 " pdb=" CG LYS A 161 " ideal model delta sigma weight residual 114.10 122.41 -8.31 2.00e+00 2.50e-01 1.73e+01 angle pdb=" PB GTP P 1 " pdb=" O3B GTP P 1 " pdb=" PG GTP P 1 " ideal model delta sigma weight residual 120.50 131.84 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " ideal model delta sigma weight residual 112.70 123.89 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C TYR A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta sigma weight residual 120.65 115.88 4.77 1.32e+00 5.74e-01 1.30e+01 ... (remaining 4292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 1660 17.58 - 35.16: 166 35.16 - 52.73: 44 52.73 - 70.31: 16 70.31 - 87.88: 7 Dihedral angle restraints: 1893 sinusoidal: 895 harmonic: 998 Sorted by residual: dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.55 -74.28 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" C8 GTP P 1 " pdb=" C1' GTP P 1 " pdb=" N9 GTP P 1 " pdb=" O4' GTP P 1 " ideal model delta sinusoidal sigma weight residual 104.59 42.71 61.88 1 2.00e+01 2.50e-03 1.27e+01 dihedral pdb=" CA GLU A 114 " pdb=" C GLU A 114 " pdb=" N LYS A 115 " pdb=" CA LYS A 115 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 274 0.040 - 0.079: 101 0.079 - 0.118: 44 0.118 - 0.158: 22 0.158 - 0.197: 10 Chirality restraints: 451 Sorted by residual: chirality pdb=" CA MET A 281 " pdb=" N MET A 281 " pdb=" C MET A 281 " pdb=" CB MET A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LEU A 336 " pdb=" N LEU A 336 " pdb=" C LEU A 336 " pdb=" CB LEU A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA MET A 307 " pdb=" N MET A 307 " pdb=" C MET A 307 " pdb=" CB MET A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.82e-01 ... (remaining 448 not shown) Planarity restraints: 506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 145 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 146 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 203 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.58e+00 pdb=" N PRO A 204 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 314 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 315 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " -0.032 5.00e-02 4.00e+02 ... (remaining 503 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 370 2.75 - 3.29: 2900 3.29 - 3.83: 5630 3.83 - 4.36: 6468 4.36 - 4.90: 10319 Nonbonded interactions: 25687 Sorted by model distance: nonbonded pdb=" OD1 ASP A 8 " pdb=" OH TYR A 89 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR A 55 " pdb=" OH TYR A 66 " model vdw 2.305 2.440 nonbonded pdb=" O LEU A 268 " pdb=" NE1 TRP A 294 " model vdw 2.370 2.520 nonbonded pdb=" NE2 GLN A 195 " pdb=" OG1 THR A 209 " model vdw 2.380 2.520 nonbonded pdb=" N ASP A 84 " pdb=" OD1 ASP A 84 " model vdw 2.384 2.520 ... (remaining 25682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 7.110 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:2.990 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: 0.5760 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 0.049 3142 Z= 0.333 Angle : 1.051 11.340 4297 Z= 0.584 Chirality : 0.059 0.197 451 Planarity : 0.008 0.064 506 Dihedral : 16.243 87.883 1251 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.33 % Allowed : 14.29 % Favored : 85.38 % 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: -2.71 (0.41), residues: 337 helix: -2.26 (0.37), residues: 116 sheet: -1.88 (0.68), residues: 51 loop : -1.29 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 266 HIS 0.002 0.001 HIS A 71 PHE 0.010 0.002 PHE A 293 TYR 0.015 0.002 TYR A 321 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TRP cc_start: 0.4145 (m100) cc_final: 0.3613 (m100) REVERT: A 87 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5065 (mtt180) REVERT: A 91 PHE cc_start: 0.6079 (t80) cc_final: 0.5870 (t80) REVERT: A 95 LYS cc_start: 0.7872 (tttt) cc_final: 0.6654 (mmmt) REVERT: A 137 ILE cc_start: 0.6298 (mm) cc_final: 0.5943 (tp) REVERT: A 147 LYS cc_start: 0.5333 (mmtt) cc_final: 0.5107 (tptt) REVERT: A 158 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 176 SER cc_start: 0.4986 (m) cc_final: 0.4551 (p) REVERT: A 177 GLU cc_start: 0.6151 (tt0) cc_final: 0.5704 (mp0) REVERT: A 183 PRO cc_start: 0.5777 (Cg_exo) cc_final: 0.5370 (Cg_endo) REVERT: A 197 ARG cc_start: 0.5058 (tpt170) cc_final: 0.4838 (tpt170) REVERT: A 238 ASP cc_start: 0.6641 (m-30) cc_final: 0.6287 (t0) REVERT: A 258 VAL cc_start: 0.7790 (t) cc_final: 0.7587 (t) REVERT: A 264 ARG cc_start: 0.6642 (ptt180) cc_final: 0.6262 (ptt180) REVERT: A 266 TRP cc_start: 0.7664 (m100) cc_final: 0.7348 (m100) REVERT: A 267 VAL cc_start: 0.7865 (t) cc_final: 0.7545 (t) REVERT: A 279 LYS cc_start: 0.8305 (tttt) cc_final: 0.7956 (mtpp) REVERT: A 292 MET cc_start: 0.8457 (tmm) cc_final: 0.8071 (tpt) REVERT: A 322 MET cc_start: 0.7559 (mmt) cc_final: 0.7007 (ptp) REVERT: A 334 MET cc_start: 0.1537 (mmt) cc_final: 0.0137 (ttp) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.2094 time to fit residues: 23.3674 Evaluate side-chains 51 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3142 Z= 0.256 Angle : 0.703 6.476 4297 Z= 0.362 Chirality : 0.048 0.210 451 Planarity : 0.007 0.054 506 Dihedral : 15.293 78.627 519 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.65 % Allowed : 17.61 % Favored : 78.74 % 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: -1.30 (0.43), residues: 337 helix: -0.42 (0.48), residues: 100 sheet: -1.49 (0.77), residues: 46 loop : -0.88 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 294 HIS 0.007 0.002 HIS A 64 PHE 0.016 0.003 PHE A 241 TYR 0.013 0.002 TYR A 213 ARG 0.003 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6663 (tmt-80) cc_final: 0.4437 (mtt180) REVERT: A 95 LYS cc_start: 0.8167 (tttt) cc_final: 0.7123 (mmmt) REVERT: A 127 LEU cc_start: 0.3987 (OUTLIER) cc_final: 0.3782 (mm) REVERT: A 153 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7212 (tp) REVERT: A 158 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6899 (mp0) REVERT: A 176 SER cc_start: 0.6102 (m) cc_final: 0.5627 (t) REVERT: A 177 GLU cc_start: 0.6238 (tt0) cc_final: 0.5824 (mp0) REVERT: A 224 ARG cc_start: 0.5656 (mtm-85) cc_final: 0.5199 (ptp-170) REVERT: A 238 ASP cc_start: 0.7133 (m-30) cc_final: 0.6674 (t0) REVERT: A 266 TRP cc_start: 0.7155 (m100) cc_final: 0.5901 (m100) REVERT: A 273 ARG cc_start: 0.3633 (mtt180) cc_final: 0.1489 (ttt180) REVERT: A 279 LYS cc_start: 0.8273 (tttt) cc_final: 0.7891 (mtpp) REVERT: A 305 ASN cc_start: 0.7612 (t0) cc_final: 0.7402 (m-40) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.2324 time to fit residues: 15.8285 Evaluate side-chains 51 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3142 Z= 0.162 Angle : 0.600 6.471 4297 Z= 0.304 Chirality : 0.044 0.137 451 Planarity : 0.006 0.048 506 Dihedral : 14.783 80.774 515 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.65 % Allowed : 19.93 % Favored : 76.41 % 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: -0.84 (0.45), residues: 337 helix: 0.40 (0.52), residues: 101 sheet: -1.52 (0.65), residues: 63 loop : -0.66 (0.46), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 266 HIS 0.005 0.001 HIS A 134 PHE 0.012 0.002 PHE A 260 TYR 0.009 0.001 TYR A 207 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.4380 (mtt180) REVERT: A 95 LYS cc_start: 0.8058 (tttt) cc_final: 0.6947 (mmmt) REVERT: A 147 LYS cc_start: 0.5403 (OUTLIER) cc_final: 0.5161 (tptt) REVERT: A 153 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7143 (tp) REVERT: A 158 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6947 (mp0) REVERT: A 176 SER cc_start: 0.6133 (m) cc_final: 0.5646 (t) REVERT: A 177 GLU cc_start: 0.6109 (tt0) cc_final: 0.5728 (mp0) REVERT: A 238 ASP cc_start: 0.7026 (m-30) cc_final: 0.6709 (t0) REVERT: A 266 TRP cc_start: 0.7538 (m100) cc_final: 0.6196 (m100) REVERT: A 279 LYS cc_start: 0.8135 (tttt) cc_final: 0.7841 (mtpt) REVERT: A 319 MET cc_start: 0.7983 (mpp) cc_final: 0.7426 (mpp) REVERT: A 334 MET cc_start: 0.1335 (OUTLIER) cc_final: -0.0046 (ttp) outliers start: 11 outliers final: 1 residues processed: 49 average time/residue: 0.2100 time to fit residues: 12.2859 Evaluate side-chains 44 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3142 Z= 0.221 Angle : 0.667 7.120 4297 Z= 0.341 Chirality : 0.046 0.158 451 Planarity : 0.007 0.062 506 Dihedral : 15.143 81.957 515 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.98 % Allowed : 18.27 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.44), residues: 337 helix: 0.19 (0.50), residues: 107 sheet: -1.48 (0.63), residues: 63 loop : -1.02 (0.45), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 266 HIS 0.005 0.002 HIS A 274 PHE 0.013 0.002 PHE A 241 TYR 0.014 0.002 TYR A 231 ARG 0.005 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.4402 (mtt180) REVERT: A 91 PHE cc_start: 0.6481 (t80) cc_final: 0.6219 (t80) REVERT: A 95 LYS cc_start: 0.8210 (tttt) cc_final: 0.7179 (mmmt) REVERT: A 147 LYS cc_start: 0.5574 (OUTLIER) cc_final: 0.5261 (tptt) REVERT: A 153 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7085 (tp) REVERT: A 161 LYS cc_start: 0.6908 (tptp) cc_final: 0.6693 (tppt) REVERT: A 175 ILE cc_start: 0.0095 (OUTLIER) cc_final: -0.0399 (tp) REVERT: A 177 GLU cc_start: 0.6148 (tt0) cc_final: 0.5703 (mp0) REVERT: A 238 ASP cc_start: 0.7129 (m-30) cc_final: 0.6733 (t0) REVERT: A 279 LYS cc_start: 0.8211 (tttt) cc_final: 0.7724 (mtpp) REVERT: A 292 MET cc_start: 0.8638 (tmm) cc_final: 0.8391 (tmm) REVERT: A 305 ASN cc_start: 0.7453 (t0) cc_final: 0.7056 (m-40) REVERT: A 306 ASP cc_start: 0.7922 (m-30) cc_final: 0.7000 (t0) REVERT: A 307 MET cc_start: 0.7757 (ttm) cc_final: 0.7432 (ttm) REVERT: A 319 MET cc_start: 0.7908 (mpp) cc_final: 0.7569 (mpp) REVERT: A 328 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7153 (tm130) outliers start: 18 outliers final: 9 residues processed: 55 average time/residue: 0.1809 time to fit residues: 11.8016 Evaluate side-chains 51 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 112 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3142 Z= 0.210 Angle : 0.644 6.298 4297 Z= 0.327 Chirality : 0.046 0.152 451 Planarity : 0.006 0.066 506 Dihedral : 15.244 83.363 515 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.32 % Allowed : 20.93 % Favored : 74.75 % 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: -1.24 (0.43), residues: 337 helix: 0.26 (0.50), residues: 108 sheet: -1.36 (0.64), residues: 59 loop : -1.29 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 6 HIS 0.005 0.002 HIS A 274 PHE 0.012 0.002 PHE A 260 TYR 0.010 0.001 TYR A 54 ARG 0.003 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.4471 (mtt180) REVERT: A 91 PHE cc_start: 0.6463 (t80) cc_final: 0.6163 (t80) REVERT: A 95 LYS cc_start: 0.8151 (tttt) cc_final: 0.7087 (mmmt) REVERT: A 147 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.5190 (mtmt) REVERT: A 153 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6960 (tp) REVERT: A 161 LYS cc_start: 0.6850 (tptp) cc_final: 0.6637 (tppt) REVERT: A 238 ASP cc_start: 0.7002 (m-30) cc_final: 0.6631 (t0) REVERT: A 279 LYS cc_start: 0.8214 (tttt) cc_final: 0.7728 (mtpp) REVERT: A 305 ASN cc_start: 0.7554 (t0) cc_final: 0.7206 (m-40) REVERT: A 306 ASP cc_start: 0.7973 (m-30) cc_final: 0.6979 (t0) REVERT: A 307 MET cc_start: 0.7796 (ttm) cc_final: 0.7422 (ttm) REVERT: A 319 MET cc_start: 0.7954 (mpp) cc_final: 0.7583 (mpp) REVERT: A 328 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 334 MET cc_start: 0.1043 (OUTLIER) cc_final: -0.0247 (ttp) outliers start: 13 outliers final: 4 residues processed: 50 average time/residue: 0.1915 time to fit residues: 11.2276 Evaluate side-chains 45 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3142 Z= 0.142 Angle : 0.583 6.577 4297 Z= 0.292 Chirality : 0.043 0.134 451 Planarity : 0.005 0.038 506 Dihedral : 14.916 86.367 515 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.32 % Allowed : 23.26 % Favored : 73.42 % 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: -0.86 (0.44), residues: 337 helix: 0.62 (0.51), residues: 108 sheet: -1.09 (0.62), residues: 64 loop : -1.11 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 6 HIS 0.004 0.001 HIS A 134 PHE 0.010 0.001 PHE A 260 TYR 0.007 0.001 TYR A 54 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8015 (tttt) cc_final: 0.7080 (tppt) REVERT: A 147 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.5284 (tptt) REVERT: A 153 LEU cc_start: 0.7364 (mp) cc_final: 0.7043 (tp) REVERT: A 161 LYS cc_start: 0.6881 (tptp) cc_final: 0.6655 (tppt) REVERT: A 200 LYS cc_start: 0.2904 (ttpp) cc_final: 0.2259 (mmtp) REVERT: A 238 ASP cc_start: 0.6990 (m-30) cc_final: 0.6713 (t0) REVERT: A 279 LYS cc_start: 0.8195 (tttt) cc_final: 0.7790 (mtpp) REVERT: A 292 MET cc_start: 0.8440 (tmm) cc_final: 0.7810 (tmm) REVERT: A 305 ASN cc_start: 0.7471 (t0) cc_final: 0.7131 (m-40) REVERT: A 306 ASP cc_start: 0.8022 (m-30) cc_final: 0.6996 (t0) REVERT: A 307 MET cc_start: 0.7801 (ttm) cc_final: 0.7490 (ttm) REVERT: A 319 MET cc_start: 0.7912 (mpp) cc_final: 0.7375 (mpp) REVERT: A 322 MET cc_start: 0.6642 (ptt) cc_final: 0.6409 (ptt) REVERT: A 334 MET cc_start: 0.1225 (OUTLIER) cc_final: -0.0223 (ttp) outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 0.1940 time to fit residues: 11.2769 Evaluate side-chains 46 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3142 Z= 0.134 Angle : 0.571 6.703 4297 Z= 0.284 Chirality : 0.043 0.129 451 Planarity : 0.005 0.037 506 Dihedral : 14.666 86.947 515 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.33 % Allowed : 23.92 % Favored : 73.75 % 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: -0.57 (0.44), residues: 337 helix: 0.93 (0.51), residues: 107 sheet: -0.71 (0.65), residues: 63 loop : -1.08 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 154 HIS 0.004 0.001 HIS A 134 PHE 0.010 0.001 PHE A 260 TYR 0.009 0.001 TYR A 54 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8034 (tttt) cc_final: 0.7083 (tppt) REVERT: A 147 LYS cc_start: 0.5301 (mmtt) cc_final: 0.5092 (tptt) REVERT: A 153 LEU cc_start: 0.7372 (mp) cc_final: 0.7048 (tp) REVERT: A 161 LYS cc_start: 0.6908 (tptp) cc_final: 0.6631 (tppt) REVERT: A 200 LYS cc_start: 0.2960 (ttpp) cc_final: 0.2425 (mmtp) REVERT: A 238 ASP cc_start: 0.6925 (m-30) cc_final: 0.6590 (t0) REVERT: A 279 LYS cc_start: 0.8186 (tttt) cc_final: 0.7846 (mtpp) REVERT: A 292 MET cc_start: 0.8422 (tmm) cc_final: 0.7713 (tmm) REVERT: A 305 ASN cc_start: 0.7571 (t0) cc_final: 0.7350 (m-40) REVERT: A 307 MET cc_start: 0.7719 (ttm) cc_final: 0.7467 (ttm) REVERT: A 319 MET cc_start: 0.7880 (mpp) cc_final: 0.7532 (mpp) REVERT: A 320 GLU cc_start: 0.8595 (tm-30) cc_final: 0.7614 (mt-10) REVERT: A 334 MET cc_start: 0.2295 (mmt) cc_final: 0.0650 (ttp) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.2035 time to fit residues: 11.5372 Evaluate side-chains 42 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3142 Z= 0.219 Angle : 0.643 6.493 4297 Z= 0.331 Chirality : 0.045 0.152 451 Planarity : 0.006 0.070 506 Dihedral : 14.947 87.014 515 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.65 % Allowed : 22.92 % Favored : 73.42 % 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: -0.79 (0.44), residues: 337 helix: 0.85 (0.52), residues: 107 sheet: -1.06 (0.65), residues: 59 loop : -1.19 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 53 HIS 0.005 0.002 HIS A 274 PHE 0.008 0.002 PHE A 260 TYR 0.013 0.001 TYR A 54 ARG 0.010 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.4784 (mtt180) REVERT: A 91 PHE cc_start: 0.6563 (t80) cc_final: 0.6219 (t80) REVERT: A 95 LYS cc_start: 0.8133 (tttt) cc_final: 0.7057 (mmmt) REVERT: A 147 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5452 (tptt) REVERT: A 153 LEU cc_start: 0.7357 (mp) cc_final: 0.6944 (tp) REVERT: A 161 LYS cc_start: 0.6959 (tptp) cc_final: 0.6678 (tppt) REVERT: A 200 LYS cc_start: 0.2745 (ttpp) cc_final: 0.2264 (mmtp) REVERT: A 238 ASP cc_start: 0.7035 (m-30) cc_final: 0.6636 (t0) REVERT: A 279 LYS cc_start: 0.8174 (tttt) cc_final: 0.7741 (mtpp) REVERT: A 292 MET cc_start: 0.8390 (tmm) cc_final: 0.7660 (tmm) REVERT: A 305 ASN cc_start: 0.7594 (t0) cc_final: 0.7334 (m-40) REVERT: A 307 MET cc_start: 0.7878 (ttm) cc_final: 0.7557 (ttm) REVERT: A 319 MET cc_start: 0.7974 (mpp) cc_final: 0.7409 (mpp) REVERT: A 334 MET cc_start: 0.1022 (OUTLIER) cc_final: -0.0211 (ttp) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.2146 time to fit residues: 11.3921 Evaluate side-chains 49 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 334 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 0.0270 chunk 25 optimal weight: 10.0000 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3142 Z= 0.156 Angle : 0.592 7.250 4297 Z= 0.300 Chirality : 0.043 0.137 451 Planarity : 0.005 0.037 506 Dihedral : 14.483 89.039 515 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.33 % Allowed : 24.92 % Favored : 72.76 % 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: -0.69 (0.45), residues: 337 helix: 1.07 (0.52), residues: 106 sheet: -1.02 (0.66), residues: 59 loop : -1.21 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 154 HIS 0.003 0.001 HIS A 274 PHE 0.007 0.001 PHE A 260 TYR 0.008 0.001 TYR A 54 ARG 0.003 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.4770 (mtt180) REVERT: A 91 PHE cc_start: 0.6576 (t80) cc_final: 0.6240 (t80) REVERT: A 95 LYS cc_start: 0.7999 (tttt) cc_final: 0.6847 (mmmt) REVERT: A 147 LYS cc_start: 0.5567 (mmtt) cc_final: 0.5277 (tptt) REVERT: A 153 LEU cc_start: 0.7411 (mp) cc_final: 0.6985 (tp) REVERT: A 161 LYS cc_start: 0.6970 (tptp) cc_final: 0.6685 (tppt) REVERT: A 238 ASP cc_start: 0.7003 (m-30) cc_final: 0.6751 (t0) REVERT: A 279 LYS cc_start: 0.8239 (tttt) cc_final: 0.7817 (mtpp) REVERT: A 292 MET cc_start: 0.8386 (tmm) cc_final: 0.7618 (tmm) REVERT: A 305 ASN cc_start: 0.7573 (t0) cc_final: 0.7339 (m-40) REVERT: A 307 MET cc_start: 0.7828 (ttm) cc_final: 0.7533 (ttm) REVERT: A 319 MET cc_start: 0.8004 (mpp) cc_final: 0.7489 (mpp) REVERT: A 334 MET cc_start: 0.1481 (mmt) cc_final: 0.0031 (ttp) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.2156 time to fit residues: 11.3777 Evaluate side-chains 42 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3142 Z= 0.178 Angle : 0.609 6.912 4297 Z= 0.311 Chirality : 0.044 0.149 451 Planarity : 0.005 0.047 506 Dihedral : 14.515 88.451 515 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.66 % Allowed : 24.25 % Favored : 73.09 % 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: -0.80 (0.44), residues: 337 helix: 0.91 (0.51), residues: 107 sheet: -1.09 (0.65), residues: 59 loop : -1.26 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 53 HIS 0.005 0.002 HIS A 274 PHE 0.007 0.001 PHE A 260 TYR 0.010 0.001 TYR A 54 ARG 0.003 0.000 ARG A 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 674 Ramachandran restraints generated. 337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 HIS cc_start: 0.7937 (m-70) cc_final: 0.6820 (p-80) REVERT: A 87 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.4781 (mtt180) REVERT: A 91 PHE cc_start: 0.6559 (t80) cc_final: 0.6178 (t80) REVERT: A 95 LYS cc_start: 0.8066 (tttt) cc_final: 0.6991 (mmmt) REVERT: A 147 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.5260 (tptt) REVERT: A 161 LYS cc_start: 0.6988 (tptp) cc_final: 0.6698 (tppt) REVERT: A 238 ASP cc_start: 0.6963 (m-30) cc_final: 0.6658 (t0) REVERT: A 279 LYS cc_start: 0.8248 (tttt) cc_final: 0.7747 (mtpp) REVERT: A 292 MET cc_start: 0.8326 (tmm) cc_final: 0.7539 (tmm) REVERT: A 305 ASN cc_start: 0.7527 (t0) cc_final: 0.7307 (m-40) REVERT: A 307 MET cc_start: 0.7884 (ttm) cc_final: 0.7566 (ttm) REVERT: A 319 MET cc_start: 0.8092 (mpp) cc_final: 0.7685 (mpp) REVERT: A 334 MET cc_start: 0.1372 (mmt) cc_final: -0.0112 (ttp) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.2091 time to fit residues: 10.6548 Evaluate side-chains 44 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.0870 chunk 12 optimal weight: 9.9990 chunk 34 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.131159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.116584 restraints weight = 11384.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.116978 restraints weight = 9252.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.117010 restraints weight = 7667.842| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3142 Z= 0.142 Angle : 0.566 6.391 4297 Z= 0.288 Chirality : 0.043 0.136 451 Planarity : 0.005 0.036 506 Dihedral : 14.326 89.479 515 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.99 % Allowed : 24.92 % Favored : 73.09 % 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: -0.70 (0.45), residues: 337 helix: 1.00 (0.51), residues: 108 sheet: -1.02 (0.65), residues: 59 loop : -1.21 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 53 HIS 0.004 0.001 HIS A 274 PHE 0.008 0.001 PHE A 194 TYR 0.008 0.001 TYR A 54 ARG 0.003 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1078.17 seconds wall clock time: 20 minutes 8.26 seconds (1208.26 seconds total)