Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 17:19:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_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_24794/07_2023/7s15_24794_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/07_2023/7s15_24794_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 2.05, per 1000 atoms: 0.64 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: 1.36 Conformation dependent library (CDL) restraints added in 445.4 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: 0.33 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: 0.73 Time building geometry restraints manager: 1.47 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: 153 45.95 - 68.92: 19 68.92 - 91.89: 6 91.89 - 114.86: 4 Dihedral angle restraints: 1896 sinusoidal: 765 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 1893 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: 0.000 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: 0.000 Extract box with map and model: 1.120 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.140 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- 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 : 17.812 114.862 1152 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 % 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 *********************** 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 : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1678 time to fit residues: 18.9491 Evaluate side-chains 66 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4874 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 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: 1.9784 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.2086 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= 0.202 Angle : 0.705 6.941 4511 Z= 0.346 Chirality : 0.041 0.171 486 Planarity : 0.004 0.045 551 Dihedral : 12.559 114.941 434 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 2.05 % 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: -2.52 (0.42), residues: 376 helix: -0.66 (0.33), residues: 244 sheet: None (None), residues: 0 loop : -3.63 (0.48), residues: 132 *********************** 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 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 82 average time/residue: 0.1188 time to fit residues: 12.3793 Evaluate side-chains 72 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0325 time to fit residues: 0.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 211 GLN R 221 GLN R 240 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3309 Z= 0.218 Angle : 0.651 6.078 4511 Z= 0.327 Chirality : 0.041 0.120 486 Planarity : 0.004 0.037 551 Dihedral : 10.851 108.032 434 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer Outliers : 3.80 % 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: -1.89 (0.43), residues: 376 helix: -0.20 (0.34), residues: 244 sheet: None (None), residues: 0 loop : -3.30 (0.50), residues: 132 *********************** 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 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 0.1306 time to fit residues: 12.2689 Evaluate side-chains 69 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0361 time to fit residues: 0.8013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- 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: 0.7770 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3309 Z= 0.268 Angle : 0.671 6.125 4511 Z= 0.339 Chirality : 0.041 0.116 486 Planarity : 0.004 0.032 551 Dihedral : 10.717 106.027 434 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.44), residues: 376 helix: -0.04 (0.34), residues: 244 sheet: None (None), residues: 0 loop : -3.14 (0.51), residues: 132 *********************** 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 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 0.1494 time to fit residues: 12.9815 Evaluate side-chains 65 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0364 time to fit residues: 0.7845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 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: 0.7758 moved from start: 0.3091 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= 0.228 Angle : 0.649 6.323 4511 Z= 0.325 Chirality : 0.040 0.147 486 Planarity : 0.004 0.031 551 Dihedral : 10.407 102.115 434 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 2.05 % 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: -1.36 (0.45), residues: 376 helix: 0.19 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -3.05 (0.51), residues: 132 *********************** 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 72 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.1245 time to fit residues: 10.9829 Evaluate side-chains 64 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0319 time to fit residues: 0.6691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.3364 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= 0.208 Angle : 0.642 6.706 4511 Z= 0.319 Chirality : 0.040 0.111 486 Planarity : 0.003 0.032 551 Dihedral : 10.233 100.347 434 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 2.92 % 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: -1.22 (0.45), residues: 376 helix: 0.30 (0.35), residues: 245 sheet: None (None), residues: 0 loop : -3.02 (0.52), residues: 131 *********************** 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 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1149 time to fit residues: 10.9510 Evaluate side-chains 64 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0369 time to fit residues: 0.8629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.0040 overall best weight: 2.3796 ------------------------------------------------------------------------------- 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: 0.3513 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= 0.197 Angle : 0.639 6.775 4511 Z= 0.317 Chirality : 0.040 0.132 486 Planarity : 0.003 0.031 551 Dihedral : 10.001 97.471 434 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.45), residues: 376 helix: 0.32 (0.35), residues: 244 sheet: None (None), residues: 0 loop : -2.84 (0.53), residues: 132 *********************** 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 71 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.1237 time to fit residues: 10.8841 Evaluate side-chains 65 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0354 time to fit residues: 0.7414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3309 Z= 0.198 Angle : 0.653 7.910 4511 Z= 0.319 Chirality : 0.040 0.128 486 Planarity : 0.005 0.075 551 Dihedral : 9.835 94.240 434 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 1.17 % 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: -1.00 (0.46), residues: 376 helix: 0.39 (0.35), residues: 248 sheet: -3.31 (1.76), residues: 12 loop : -2.64 (0.58), residues: 116 *********************** 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 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.1284 time to fit residues: 11.8406 Evaluate side-chains 67 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0424 time to fit residues: 0.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 300 ASN ** 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: 0.7725 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3309 Z= 0.228 Angle : 0.677 7.350 4511 Z= 0.333 Chirality : 0.042 0.133 486 Planarity : 0.004 0.068 551 Dihedral : 9.934 95.723 434 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 0.88 % 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: -1.10 (0.46), residues: 376 helix: 0.23 (0.34), residues: 248 sheet: -3.03 (1.85), residues: 12 loop : -2.51 (0.60), residues: 116 *********************** 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 66 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1319 time to fit residues: 10.8392 Evaluate side-chains 63 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0316 time to fit residues: 0.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.0010 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 3309 Z= 0.199 Angle : 0.703 10.275 4511 Z= 0.337 Chirality : 0.043 0.292 486 Planarity : 0.005 0.078 551 Dihedral : 9.760 92.944 434 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.58 % 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: -1.10 (0.45), residues: 376 helix: 0.19 (0.34), residues: 248 sheet: -2.87 (1.93), residues: 12 loop : -2.44 (0.60), residues: 116 ********************** 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 66 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.1318 time to fit residues: 10.6819 Evaluate side-chains 65 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0378 time to fit residues: 0.6223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.126043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.111315 restraints weight = 8689.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114349 restraints weight = 4437.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.116344 restraints weight = 2687.676| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3309 Z= 0.173 Angle : 0.670 9.210 4511 Z= 0.320 Chirality : 0.042 0.263 486 Planarity : 0.004 0.070 551 Dihedral : 9.359 86.261 434 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 0.58 % 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: -1.02 (0.45), residues: 376 helix: 0.32 (0.34), residues: 248 sheet: -3.60 (1.55), residues: 12 loop : -2.48 (0.60), residues: 116 =============================================================================== Job complete usr+sys time: 918.62 seconds wall clock time: 17 minutes 12.79 seconds (1032.79 seconds total)