Starting phenix.real_space_refine on Wed Jan 17 12:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/01_2024/7s15_24794_updated.pdb" } resolution = 3.8 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= 0.060 sd= 0.638 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: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2117 2.51 5 N 525 2.21 5 O 545 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 34": "OE1" <-> "OE2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ASP 53": "OD1" <-> "OD2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 122": "OD1" <-> "OD2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R ASP 293": "OD1" <-> "OD2" Residue "R ASP 372": "OD1" <-> "OD2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R GLU 387": "OE1" <-> "OE2" Residue "R TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 408": "OE1" <-> "OE2" Residue "R ARG 421": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 3207 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3207 Unusual residues: {'82L': 1} Classifications: {'peptide': 382, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 367, None: 1} Not linked: pdbres="ARG R 421 " pdbres="82L R 501 " Chain breaks: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.70 Number of scatterers: 3207 At special positions: 0 Unit cell: (65.296, 65.296, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 F 2 9.00 O 545 8.00 N 525 7.00 C 2117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.05 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 1.32 Conformation dependent library (CDL) restraints added in 661.4 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 0 sheets defined 58.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.649A pdb=" N ARG R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 139 through 165 removed outlier: 3.810A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 removed outlier: 3.925A pdb=" N ALA R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 220 Processing helix chain 'R' and resid 226 through 253 removed outlier: 3.698A pdb=" N TYR R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 244 " --> pdb=" O ASN R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 279 removed outlier: 3.518A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 282 through 291 removed outlier: 4.083A pdb=" N LEU R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 334 Processing helix chain 'R' and resid 346 through 359 removed outlier: 4.333A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER R 352 " --> pdb=" O ARG R 348 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 364 through 370 Processing helix chain 'R' and resid 378 through 403 removed outlier: 4.098A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL R 398 " --> pdb=" O GLN R 394 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 420 removed outlier: 3.861A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 429 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: 0.74 Time building geometry restraints manager: 1.43 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: 972 1.34 - 1.46: 936 1.46 - 1.58: 1378 1.58 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 3309 Sorted by residual: bond pdb=" C22 82L R 501 " pdb=" C25 82L R 501 " ideal model delta sigma weight residual 1.577 1.507 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C7 82L R 501 " pdb=" N3 82L R 501 " ideal model delta sigma weight residual 1.316 1.385 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C6 82L R 501 " pdb=" N5 82L R 501 " ideal model delta sigma weight residual 1.313 1.377 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C29 82L R 501 " pdb=" O31 82L R 501 " ideal model delta sigma weight residual 1.416 1.356 0.060 2.00e-02 2.50e+03 9.09e+00 bond pdb=" C15 82L R 501 " pdb=" N16 82L R 501 " ideal model delta sigma weight residual 1.336 1.392 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 3304 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.21: 108 107.21 - 113.93: 1828 113.93 - 120.64: 1440 120.64 - 127.36: 1073 127.36 - 134.08: 62 Bond angle restraints: 4511 Sorted by residual: angle pdb=" CA LEU R 166 " pdb=" C LEU R 166 " pdb=" N LEU R 167 " ideal model delta sigma weight residual 118.27 123.59 -5.32 1.59e+00 3.96e-01 1.12e+01 angle pdb=" CA CYS R 126 " pdb=" CB CYS R 126 " pdb=" SG CYS R 126 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 angle pdb=" C18 82L R 501 " pdb=" C17 82L R 501 " pdb=" N9 82L R 501 " ideal model delta sigma weight residual 114.40 123.70 -9.30 3.00e+00 1.11e-01 9.61e+00 angle pdb=" N30 82L R 501 " pdb=" C29 82L R 501 " pdb=" O31 82L R 501 " ideal model delta sigma weight residual 128.56 119.82 8.74 3.00e+00 1.11e-01 8.48e+00 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.92 117.03 4.89 1.73e+00 3.34e-01 7.99e+00 ... (remaining 4506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 1714 22.97 - 45.95: 154 45.95 - 68.92: 19 68.92 - 91.89: 6 91.89 - 114.86: 6 Dihedral angle restraints: 1899 sinusoidal: 768 harmonic: 1131 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -14.81 -71.19 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 153.24 -60.24 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CA CYS R 296 " pdb=" C CYS R 296 " pdb=" N TRP R 297 " pdb=" CA TRP R 297 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 1896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 213 0.027 - 0.054: 167 0.054 - 0.081: 72 0.081 - 0.108: 21 0.108 - 0.135: 13 Chirality restraints: 486 Sorted by residual: chirality pdb=" CG LEU R 218 " pdb=" CB LEU R 218 " pdb=" CD1 LEU R 218 " pdb=" CD2 LEU R 218 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA GLN R 394 " pdb=" N GLN R 394 " pdb=" C GLN R 394 " pdb=" CB GLN R 394 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA THR R 298 " pdb=" N THR R 298 " pdb=" C THR R 298 " pdb=" CB THR R 298 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 483 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 82L R 501 " 0.315 2.00e-02 2.50e+03 1.43e-01 4.59e+02 pdb=" C33 82L R 501 " -0.165 2.00e-02 2.50e+03 pdb=" C34 82L R 501 " -0.149 2.00e-02 2.50e+03 pdb=" C35 82L R 501 " -0.048 2.00e-02 2.50e+03 pdb=" C36 82L R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C37 82L R 501 " 0.022 2.00e-02 2.50e+03 pdb=" C38 82L R 501 " -0.078 2.00e-02 2.50e+03 pdb=" F39 82L R 501 " -0.074 2.00e-02 2.50e+03 pdb=" F40 82L R 501 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 82L R 501 " -0.066 2.00e-02 2.50e+03 3.87e-02 3.00e+01 pdb=" C25 82L R 501 " 0.041 2.00e-02 2.50e+03 pdb=" C26 82L R 501 " 0.021 2.00e-02 2.50e+03 pdb=" C27 82L R 501 " -0.014 2.00e-02 2.50e+03 pdb=" C28 82L R 501 " -0.025 2.00e-02 2.50e+03 pdb=" C29 82L R 501 " 0.015 2.00e-02 2.50e+03 pdb=" N30 82L R 501 " 0.059 2.00e-02 2.50e+03 pdb=" O31 82L R 501 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 82L R 501 " 0.022 2.00e-02 2.50e+03 2.15e-02 1.39e+01 pdb=" C11 82L R 501 " 0.013 2.00e-02 2.50e+03 pdb=" C12 82L R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C13 82L R 501 " -0.026 2.00e-02 2.50e+03 pdb=" C14 82L R 501 " -0.007 2.00e-02 2.50e+03 pdb=" C15 82L R 501 " 0.019 2.00e-02 2.50e+03 pdb=" C17 82L R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C18 82L R 501 " -0.049 2.00e-02 2.50e+03 pdb=" C41 82L R 501 " -0.009 2.00e-02 2.50e+03 pdb=" C8 82L R 501 " -0.011 2.00e-02 2.50e+03 pdb=" N16 82L R 501 " 0.022 2.00e-02 2.50e+03 pdb=" N9 82L R 501 " 0.017 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 207 2.72 - 3.26: 3567 3.26 - 3.81: 5108 3.81 - 4.35: 5923 4.35 - 4.90: 9478 Nonbonded interactions: 24283 Sorted by model distance: nonbonded pdb=" OH TYR R 241 " pdb=" OE2 GLU R 364 " model vdw 2.174 2.440 nonbonded pdb=" O GLN R 47 " pdb=" OG1 THR R 51 " model vdw 2.276 2.440 nonbonded pdb=" O THR R 386 " pdb=" OG SER R 389 " model vdw 2.293 2.440 nonbonded pdb=" O LEU R 349 " pdb=" OG SER R 352 " model vdw 2.317 2.440 nonbonded pdb=" OD1 ASN R 304 " pdb=" NE1 TRP R 306 " model vdw 2.326 2.520 ... (remaining 24278 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: 0.010 Normalize map: mean=0, sd=1: 0.140 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: 0.010 Extract box with map and model: 1.010 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.620 Find NCS groups from input model: 0.090 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 3309 Z= 0.460 Angle : 0.898 9.298 4511 Z= 0.460 Chirality : 0.045 0.135 486 Planarity : 0.008 0.143 551 Dihedral : 18.371 114.862 1155 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % 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: -4.51 (0.35), residues: 376 helix: -2.23 (0.27), residues: 246 sheet: None (None), residues: 0 loop : -4.38 (0.42), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 297 HIS 0.003 0.001 HIS R 173 PHE 0.016 0.002 PHE R 143 TYR 0.015 0.002 TYR R 145 ARG 0.008 0.001 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 244 LEU cc_start: 0.9031 (mp) cc_final: 0.8820 (mp) REVERT: R 269 TYR cc_start: 0.8017 (m-10) cc_final: 0.7458 (m-80) REVERT: R 394 GLN cc_start: 0.9370 (pp30) cc_final: 0.8430 (pp30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1622 time to fit residues: 18.3272 Evaluate side-chains 66 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN R 180 HIS R 221 GLN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3309 Z= 0.215 Angle : 0.702 6.954 4511 Z= 0.349 Chirality : 0.042 0.168 486 Planarity : 0.004 0.046 551 Dihedral : 12.604 121.422 437 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.34 % Allowed : 19.59 % Favored : 78.07 % 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: -2.62 (0.42), residues: 376 helix: -0.72 (0.33), residues: 243 sheet: None (None), residues: 0 loop : -3.69 (0.47), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 297 HIS 0.003 0.001 HIS R 363 PHE 0.012 0.001 PHE R 315 TYR 0.017 0.002 TYR R 235 ARG 0.007 0.001 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 68 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8161 (mm-30) REVERT: R 221 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: R 234 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8867 (mm110) REVERT: R 394 GLN cc_start: 0.9160 (pp30) cc_final: 0.8902 (pp30) REVERT: R 404 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5801 (m-80) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.1362 time to fit residues: 13.5745 Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 221 GLN Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.0040 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3309 Z= 0.161 Angle : 0.629 6.733 4511 Z= 0.310 Chirality : 0.040 0.118 486 Planarity : 0.004 0.037 551 Dihedral : 10.482 92.355 437 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.09 % Allowed : 21.93 % Favored : 73.98 % 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: -1.78 (0.44), residues: 376 helix: -0.13 (0.34), residues: 245 sheet: None (None), residues: 0 loop : -3.25 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.010 0.001 PHE R 315 TYR 0.017 0.002 TYR R 145 ARG 0.003 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 68 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8118 (mm-30) REVERT: R 198 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7773 (t70) REVERT: R 234 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8993 (mm-40) REVERT: R 394 GLN cc_start: 0.9128 (pp30) cc_final: 0.8293 (pp30) REVERT: R 404 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.5922 (m-80) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 0.1350 time to fit residues: 14.3118 Evaluate side-chains 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0020 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN R 300 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3309 Z= 0.217 Angle : 0.659 6.937 4511 Z= 0.327 Chirality : 0.041 0.175 486 Planarity : 0.004 0.050 551 Dihedral : 9.428 86.955 437 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.56 % Allowed : 22.51 % Favored : 71.93 % 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: -1.56 (0.44), residues: 376 helix: -0.01 (0.34), residues: 245 sheet: None (None), residues: 0 loop : -3.05 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 297 HIS 0.002 0.001 HIS R 173 PHE 0.010 0.001 PHE R 315 TYR 0.025 0.002 TYR R 269 ARG 0.003 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: R 269 TYR cc_start: 0.7998 (m-10) cc_final: 0.7379 (m-80) REVERT: R 394 GLN cc_start: 0.9142 (pp30) cc_final: 0.8342 (pp30) REVERT: R 404 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5830 (m-80) outliers start: 19 outliers final: 12 residues processed: 76 average time/residue: 0.1276 time to fit residues: 12.3172 Evaluate side-chains 77 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- 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: 0.7653 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3309 Z= 0.144 Angle : 0.600 6.721 4511 Z= 0.294 Chirality : 0.039 0.113 486 Planarity : 0.004 0.041 551 Dihedral : 8.009 84.375 437 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.09 % Allowed : 26.61 % Favored : 69.30 % 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: -1.20 (0.45), residues: 376 helix: 0.24 (0.34), residues: 244 sheet: None (None), residues: 0 loop : -2.81 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 243 HIS 0.001 0.000 HIS R 99 PHE 0.009 0.001 PHE R 315 TYR 0.018 0.001 TYR R 269 ARG 0.003 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: R 269 TYR cc_start: 0.7900 (m-10) cc_final: 0.7401 (m-80) REVERT: R 394 GLN cc_start: 0.9052 (pp30) cc_final: 0.8338 (pp30) REVERT: R 404 PHE cc_start: 0.6439 (OUTLIER) cc_final: 0.5821 (m-80) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.1240 time to fit residues: 12.4966 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.0030 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3309 Z= 0.185 Angle : 0.612 6.599 4511 Z= 0.303 Chirality : 0.040 0.137 486 Planarity : 0.004 0.062 551 Dihedral : 8.153 84.042 437 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.85 % Allowed : 26.90 % Favored : 67.25 % 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: -1.04 (0.45), residues: 376 helix: 0.33 (0.35), residues: 243 sheet: None (None), residues: 0 loop : -2.64 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.002 0.000 HIS R 363 PHE 0.006 0.001 PHE R 315 TYR 0.014 0.001 TYR R 269 ARG 0.002 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 67 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: R 269 TYR cc_start: 0.7908 (m-10) cc_final: 0.7338 (m-80) REVERT: R 394 GLN cc_start: 0.9107 (pp30) cc_final: 0.8302 (pp30) REVERT: R 404 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.5842 (m-80) outliers start: 20 outliers final: 13 residues processed: 79 average time/residue: 0.1066 time to fit residues: 10.8989 Evaluate side-chains 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3309 Z= 0.269 Angle : 0.673 6.399 4511 Z= 0.337 Chirality : 0.042 0.130 486 Planarity : 0.005 0.066 551 Dihedral : 8.360 83.209 437 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 6.73 % Allowed : 25.44 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.45), residues: 376 helix: 0.25 (0.34), residues: 247 sheet: -3.42 (1.67), residues: 12 loop : -2.52 (0.59), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 243 HIS 0.003 0.001 HIS R 173 PHE 0.009 0.001 PHE R 367 TYR 0.015 0.002 TYR R 148 ARG 0.004 0.001 ARG R 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: R 64 ARG cc_start: 0.6542 (ptp-170) cc_final: 0.6049 (ptp-170) REVERT: R 269 TYR cc_start: 0.7941 (m-10) cc_final: 0.7439 (m-80) REVERT: R 288 LYS cc_start: 0.8932 (tppt) cc_final: 0.8717 (tppp) REVERT: R 394 GLN cc_start: 0.9257 (pp30) cc_final: 0.8509 (pp30) REVERT: R 404 PHE cc_start: 0.6477 (OUTLIER) cc_final: 0.5824 (m-80) outliers start: 23 outliers final: 19 residues processed: 76 average time/residue: 0.1163 time to fit residues: 11.3770 Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 53 ASP Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 397 MET Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3309 Z= 0.218 Angle : 0.648 6.531 4511 Z= 0.322 Chirality : 0.041 0.128 486 Planarity : 0.004 0.059 551 Dihedral : 8.304 85.135 437 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 6.43 % Allowed : 26.90 % Favored : 66.67 % 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: -0.96 (0.46), residues: 376 helix: 0.35 (0.35), residues: 247 sheet: -3.28 (1.68), residues: 12 loop : -2.42 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.009 0.001 PHE R 367 TYR 0.011 0.001 TYR R 269 ARG 0.002 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: R 269 TYR cc_start: 0.7870 (m-10) cc_final: 0.7341 (m-80) REVERT: R 394 GLN cc_start: 0.9226 (pp30) cc_final: 0.8533 (pp30) REVERT: R 404 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5844 (m-80) outliers start: 22 outliers final: 17 residues processed: 79 average time/residue: 0.1223 time to fit residues: 12.3589 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3309 Z= 0.228 Angle : 0.677 8.512 4511 Z= 0.329 Chirality : 0.041 0.124 486 Planarity : 0.005 0.074 551 Dihedral : 8.252 86.337 437 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.26 % Allowed : 28.65 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.46), residues: 376 helix: 0.33 (0.34), residues: 247 sheet: -3.15 (1.74), residues: 12 loop : -2.39 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.010 0.001 PHE R 393 TYR 0.028 0.002 TYR R 235 ARG 0.002 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 269 TYR cc_start: 0.7860 (m-10) cc_final: 0.7374 (m-80) REVERT: R 394 GLN cc_start: 0.9140 (pp30) cc_final: 0.8549 (pp30) REVERT: R 404 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.5886 (m-80) outliers start: 18 outliers final: 16 residues processed: 76 average time/residue: 0.1260 time to fit residues: 12.0638 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 0.0040 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3309 Z= 0.207 Angle : 0.676 7.269 4511 Z= 0.326 Chirality : 0.041 0.157 486 Planarity : 0.005 0.073 551 Dihedral : 8.148 87.205 437 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.56 % Allowed : 28.36 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.46), residues: 376 helix: 0.33 (0.35), residues: 247 sheet: -3.08 (1.78), residues: 12 loop : -2.35 (0.61), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.008 0.001 PHE R 393 TYR 0.018 0.001 TYR R 235 ARG 0.002 0.000 ARG R 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 269 TYR cc_start: 0.7847 (m-10) cc_final: 0.7357 (m-80) REVERT: R 394 GLN cc_start: 0.9148 (pp30) cc_final: 0.8465 (pp30) REVERT: R 404 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.5897 (m-80) outliers start: 19 outliers final: 17 residues processed: 78 average time/residue: 0.0963 time to fit residues: 9.6678 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 242 TYR Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 347 CYS Chi-restraints excluded: chain R residue 356 LEU Chi-restraints excluded: chain R residue 357 ILE Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 396 LEU Chi-restraints excluded: chain R residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.112881 restraints weight = 8667.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115990 restraints weight = 4360.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.117988 restraints weight = 2615.170| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3309 Z= 0.156 Angle : 0.663 9.314 4511 Z= 0.310 Chirality : 0.042 0.275 486 Planarity : 0.004 0.069 551 Dihedral : 7.827 87.926 437 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.68 % Allowed : 30.12 % Favored : 65.20 % 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: -0.88 (0.46), residues: 376 helix: 0.38 (0.34), residues: 248 sheet: -2.83 (1.90), residues: 12 loop : -2.42 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 243 HIS 0.001 0.000 HIS R 171 PHE 0.009 0.001 PHE R 367 TYR 0.011 0.001 TYR R 269 ARG 0.002 0.000 ARG R 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 964.83 seconds wall clock time: 18 minutes 18.68 seconds (1098.68 seconds total)