Starting phenix.real_space_refine on Sun Mar 10 14:38:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwe_35765/03_2024/8iwe_35765_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwe_35765/03_2024/8iwe_35765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwe_35765/03_2024/8iwe_35765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwe_35765/03_2024/8iwe_35765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwe_35765/03_2024/8iwe_35765_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwe_35765/03_2024/8iwe_35765_neut_updated.pdb" } resolution = 3.4 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= 0.002 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 12 5.16 5 C 1497 2.51 5 N 353 2.21 5 O 374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 95": "OE1" <-> "OE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 174": "OE1" <-> "OE2" Residue "R GLU 179": "OE1" <-> "OE2" Residue "R ASP 277": "OD1" <-> "OD2" Residue "R TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 2236 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2236 Unusual residues: {'SPD': 1} Classifications: {'peptide': 296, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 283, None: 1} Not linked: pdbres="LYS R 329 " pdbres="SPD R 401 " Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 1.79, per 1000 atoms: 0.80 Number of scatterers: 2236 At special positions: 0 Unit cell: (63.403, 75.905, 75.012, 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 12 16.00 O 374 8.00 N 353 7.00 C 1497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.04 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: 0.91 Conformation dependent library (CDL) restraints added in 460.7 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'R' and resid 34 through 56 removed outlier: 3.679A pdb=" N LEU R 39 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLY R 40 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU R 41 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY R 49 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU R 52 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE R 54 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE R 55 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 84 removed outlier: 3.527A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 95 Processing helix chain 'R' and resid 104 through 135 removed outlier: 4.179A pdb=" N HIS R 108 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR R 109 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP R 112 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR R 113 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N CYS R 116 " --> pdb=" O THR R 113 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR R 135 " --> pdb=" O ILE R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 146 through 168 removed outlier: 3.776A pdb=" N PHE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 231 removed outlier: 4.340A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.991A pdb=" N VAL R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 282 removed outlier: 4.395A pdb=" N LYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR R 259 " --> pdb=" O LYS R 255 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU R 260 " --> pdb=" O ALA R 256 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.772A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 311 removed outlier: 3.912A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 316 through 326 134 hydrogen bonds defined for protein. 294 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: 0.49 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 346 1.32 - 1.45: 686 1.45 - 1.57: 1255 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 2302 Sorted by residual: bond pdb=" C VAL R 94 " pdb=" O VAL R 94 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.23e-02 6.61e+03 7.83e+00 bond pdb=" CA VAL R 94 " pdb=" CB VAL R 94 " ideal model delta sigma weight residual 1.540 1.510 0.030 1.37e-02 5.33e+03 4.72e+00 bond pdb=" CA ILE R 280 " pdb=" C ILE R 280 " ideal model delta sigma weight residual 1.519 1.542 -0.023 1.14e-02 7.69e+03 4.22e+00 bond pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.39e-02 5.18e+03 3.44e+00 bond pdb=" CA TYR R 302 " pdb=" C TYR R 302 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.41e-02 5.03e+03 2.94e+00 ... (remaining 2297 not shown) Histogram of bond angle deviations from ideal: 101.17 - 107.74: 89 107.74 - 114.30: 1273 114.30 - 120.87: 1133 120.87 - 127.44: 629 127.44 - 134.00: 24 Bond angle restraints: 3148 Sorted by residual: angle pdb=" N ASN R 303 " pdb=" CA ASN R 303 " pdb=" C ASN R 303 " ideal model delta sigma weight residual 112.38 103.43 8.95 1.22e+00 6.72e-01 5.38e+01 angle pdb=" N ILE R 280 " pdb=" CA ILE R 280 " pdb=" C ILE R 280 " ideal model delta sigma weight residual 113.07 122.36 -9.29 1.36e+00 5.41e-01 4.66e+01 angle pdb=" C TYR R 315 " pdb=" N PRO R 316 " pdb=" CA PRO R 316 " ideal model delta sigma weight residual 119.84 126.85 -7.01 1.25e+00 6.40e-01 3.15e+01 angle pdb=" N PHE R 286 " pdb=" CA PHE R 286 " pdb=" C PHE R 286 " ideal model delta sigma weight residual 111.54 119.15 -7.61 1.36e+00 5.41e-01 3.13e+01 angle pdb=" N PHE R 207 " pdb=" CA PHE R 207 " pdb=" C PHE R 207 " ideal model delta sigma weight residual 111.36 116.49 -5.13 1.09e+00 8.42e-01 2.21e+01 ... (remaining 3143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1053 11.82 - 23.64: 149 23.64 - 35.45: 63 35.45 - 47.27: 30 47.27 - 59.09: 11 Dihedral angle restraints: 1306 sinusoidal: 434 harmonic: 872 Sorted by residual: dihedral pdb=" C VAL R 279 " pdb=" N VAL R 279 " pdb=" CA VAL R 279 " pdb=" CB VAL R 279 " ideal model delta harmonic sigma weight residual -122.00 -137.52 15.52 0 2.50e+00 1.60e-01 3.85e+01 dihedral pdb=" N VAL R 279 " pdb=" C VAL R 279 " pdb=" CA VAL R 279 " pdb=" CB VAL R 279 " ideal model delta harmonic sigma weight residual 123.40 133.59 -10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" N TRP R 317 " pdb=" C TRP R 317 " pdb=" CA TRP R 317 " pdb=" CB TRP R 317 " ideal model delta harmonic sigma weight residual 122.80 130.73 -7.93 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 1303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 334 0.090 - 0.180: 22 0.180 - 0.269: 6 0.269 - 0.359: 2 0.359 - 0.449: 2 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA VAL R 279 " pdb=" N VAL R 279 " pdb=" C VAL R 279 " pdb=" CB VAL R 279 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA PHE R 286 " pdb=" N PHE R 286 " pdb=" C PHE R 286 " pdb=" CB PHE R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA TRP R 317 " pdb=" N TRP R 317 " pdb=" C TRP R 317 " pdb=" CB TRP R 317 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 363 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C TYR R 301 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR R 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 147 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C SER R 147 " -0.036 2.00e-02 2.50e+03 pdb=" O SER R 147 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 148 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 95 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C GLU R 95 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU R 95 " -0.012 2.00e-02 2.50e+03 pdb=" N SER R 96 " -0.011 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 799 2.84 - 3.35: 2141 3.35 - 3.87: 3443 3.87 - 4.38: 3772 4.38 - 4.90: 6483 Nonbonded interactions: 16638 Sorted by model distance: nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 301 " model vdw 2.321 2.440 nonbonded pdb=" OD2 ASP R 281 " pdb=" OG1 THR R 288 " model vdw 2.386 2.440 nonbonded pdb=" O THR R 109 " pdb=" OG1 THR R 113 " model vdw 2.422 2.440 nonbonded pdb=" O ASP R 281 " pdb=" O MET R 284 " model vdw 2.450 3.040 nonbonded pdb=" O THR R 139 " pdb=" OG1 THR R 139 " model vdw 2.472 2.440 ... (remaining 16633 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 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.290 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.430 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.004 0.034 2302 Z= 0.259 Angle : 0.935 9.620 3148 Z= 0.641 Chirality : 0.067 0.449 366 Planarity : 0.004 0.030 385 Dihedral : 16.003 59.087 738 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.84 % Allowed : 19.43 % Favored : 77.73 % Cbeta Deviations : 0.36 % 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: -0.50 (0.52), residues: 290 helix: 0.67 (0.41), residues: 196 sheet: None (None), residues: 0 loop : -2.51 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 317 HIS 0.001 0.000 HIS R 122 PHE 0.006 0.001 PHE R 286 TYR 0.011 0.001 TYR R 99 ARG 0.002 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.255 Fit side-chains REVERT: R 255 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8416 (tttm) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.2065 time to fit residues: 7.1714 Evaluate side-chains 22 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2302 Z= 0.159 Angle : 0.517 5.302 3148 Z= 0.274 Chirality : 0.039 0.130 366 Planarity : 0.005 0.030 385 Dihedral : 7.168 59.089 328 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.32 % Allowed : 20.85 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.52), residues: 290 helix: 0.96 (0.39), residues: 203 sheet: None (None), residues: 0 loop : -2.55 (0.62), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 79 TYR 0.016 0.001 TYR R 274 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.242 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 0.1522 time to fit residues: 5.6932 Evaluate side-chains 25 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2302 Z= 0.142 Angle : 0.476 5.424 3148 Z= 0.250 Chirality : 0.037 0.109 366 Planarity : 0.005 0.037 385 Dihedral : 7.094 59.127 325 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.21 % Allowed : 20.85 % Favored : 73.93 % 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: -0.04 (0.53), residues: 290 helix: 0.95 (0.40), residues: 202 sheet: None (None), residues: 0 loop : -2.35 (0.66), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.008 0.001 TYR R 274 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.247 Fit side-chains REVERT: R 229 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8085 (ttm110) REVERT: R 258 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7492 (ttmt) outliers start: 11 outliers final: 4 residues processed: 32 average time/residue: 0.2048 time to fit residues: 7.5188 Evaluate side-chains 26 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2302 Z= 0.152 Angle : 0.492 5.432 3148 Z= 0.252 Chirality : 0.037 0.118 366 Planarity : 0.004 0.028 385 Dihedral : 4.785 36.949 324 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.74 % Allowed : 21.80 % Favored : 73.46 % 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: -0.13 (0.53), residues: 290 helix: 0.88 (0.40), residues: 202 sheet: None (None), residues: 0 loop : -2.41 (0.65), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 100 TYR 0.009 0.001 TYR R 274 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.252 Fit side-chains REVERT: R 230 LYS cc_start: 0.7572 (tppt) cc_final: 0.7179 (ttpp) REVERT: R 258 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7520 (ttmt) outliers start: 10 outliers final: 3 residues processed: 32 average time/residue: 0.2123 time to fit residues: 7.8447 Evaluate side-chains 29 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2302 Z= 0.140 Angle : 0.478 5.438 3148 Z= 0.246 Chirality : 0.037 0.122 366 Planarity : 0.004 0.022 385 Dihedral : 4.731 33.257 324 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.79 % Allowed : 21.80 % Favored : 74.41 % 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: -0.17 (0.53), residues: 290 helix: 0.85 (0.40), residues: 202 sheet: None (None), residues: 0 loop : -2.44 (0.65), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.254 Fit side-chains REVERT: R 258 LYS cc_start: 0.7894 (ttpt) cc_final: 0.7523 (ttmt) outliers start: 8 outliers final: 5 residues processed: 31 average time/residue: 0.2183 time to fit residues: 7.7210 Evaluate side-chains 30 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2302 Z= 0.141 Angle : 0.495 5.452 3148 Z= 0.249 Chirality : 0.037 0.117 366 Planarity : 0.004 0.022 385 Dihedral : 4.666 34.243 324 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.84 % Allowed : 22.75 % Favored : 74.41 % 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: -0.12 (0.53), residues: 290 helix: 0.76 (0.39), residues: 208 sheet: None (None), residues: 0 loop : -2.24 (0.67), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.005 0.001 PHE R 206 TYR 0.015 0.001 TYR R 99 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.242 Fit side-chains REVERT: R 258 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7523 (ttmt) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.2110 time to fit residues: 7.7284 Evaluate side-chains 31 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0000 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2302 Z= 0.125 Angle : 0.459 5.457 3148 Z= 0.234 Chirality : 0.037 0.118 366 Planarity : 0.004 0.021 385 Dihedral : 4.516 34.572 324 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.79 % Allowed : 22.27 % Favored : 73.93 % 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: -0.03 (0.52), residues: 290 helix: 0.82 (0.39), residues: 208 sheet: None (None), residues: 0 loop : -2.18 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.005 0.000 PHE R 206 TYR 0.015 0.001 TYR R 99 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.233 Fit side-chains REVERT: R 258 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7494 (ttmt) outliers start: 8 outliers final: 4 residues processed: 38 average time/residue: 0.2016 time to fit residues: 8.7455 Evaluate side-chains 34 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2302 Z= 0.168 Angle : 0.531 8.105 3148 Z= 0.266 Chirality : 0.037 0.117 366 Planarity : 0.004 0.020 385 Dihedral : 4.533 32.436 324 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.37 % Allowed : 24.64 % Favored : 72.99 % 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: 0.08 (0.52), residues: 290 helix: 0.92 (0.39), residues: 208 sheet: None (None), residues: 0 loop : -2.21 (0.66), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.016 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.259 Fit side-chains REVERT: R 258 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7537 (ttmt) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.2203 time to fit residues: 8.5039 Evaluate side-chains 34 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2302 Z= 0.137 Angle : 0.489 5.807 3148 Z= 0.246 Chirality : 0.037 0.117 366 Planarity : 0.004 0.020 385 Dihedral : 4.634 34.699 324 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.37 % Allowed : 25.12 % Favored : 72.51 % 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: 0.16 (0.52), residues: 290 helix: 1.12 (0.39), residues: 202 sheet: None (None), residues: 0 loop : -2.35 (0.64), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 317 HIS 0.000 0.000 HIS R 59 PHE 0.005 0.001 PHE R 206 TYR 0.017 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.251 Fit side-chains REVERT: R 258 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7522 (ttmt) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.1939 time to fit residues: 7.4128 Evaluate side-chains 34 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 16 optimal weight: 0.0040 chunk 26 optimal weight: 8.9990 overall best weight: 0.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2302 Z= 0.119 Angle : 0.476 6.246 3148 Z= 0.238 Chirality : 0.036 0.117 366 Planarity : 0.004 0.021 385 Dihedral : 4.485 34.678 324 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.42 % Allowed : 25.59 % Favored : 72.99 % 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: 0.51 (0.53), residues: 290 helix: 1.35 (0.40), residues: 197 sheet: None (None), residues: 0 loop : -1.93 (0.65), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.003 0.000 PHE R 206 TYR 0.017 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.244 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.2059 time to fit residues: 7.7683 Evaluate side-chains 33 residues out of total 253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093616 restraints weight = 4040.061| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.03 r_work: 0.3147 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2302 Z= 0.137 Angle : 0.505 8.667 3148 Z= 0.255 Chirality : 0.037 0.128 366 Planarity : 0.004 0.020 385 Dihedral : 4.443 33.178 324 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.90 % Allowed : 25.12 % Favored : 72.99 % 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: 0.41 (0.53), residues: 290 helix: 1.30 (0.39), residues: 202 sheet: None (None), residues: 0 loop : -2.23 (0.65), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.005 0.001 PHE R 206 TYR 0.016 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 909.64 seconds wall clock time: 17 minutes 9.95 seconds (1029.95 seconds total)