Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:15:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_24794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_24794.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_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_24794/11_2022/7s15_24794_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_24794_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_24794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_24794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_24794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s15_24794/11_2022/7s15_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 Convert atoms to be neutral 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-dev-4778/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: 2.33, per 1000 atoms: 0.73 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: 1.30 Conformation dependent library (CDL) restraints added in 498.2 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: 0.32 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: 1.42 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 1.598 1.507 0.091 2.00e-02 2.50e+03 2.05e+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=" C12 82L R 501 " pdb=" C41 82L R 501 " ideal model delta sigma weight residual 1.552 1.485 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C17 82L R 501 " pdb=" C18 82L R 501 " ideal model delta sigma weight residual 1.557 1.491 0.066 2.00e-02 2.50e+03 1.09e+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 ... (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=" C18 82L R 501 " pdb=" C17 82L R 501 " pdb=" N9 82L R 501 " ideal model delta sigma weight residual 149.60 123.70 25.90 3.00e+00 1.11e-01 7.45e+01 angle pdb=" C18 82L R 501 " pdb=" C17 82L R 501 " pdb=" N16 82L R 501 " ideal model delta sigma weight residual 101.95 123.40 -21.45 3.00e+00 1.11e-01 5.11e+01 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=" 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 - 18.00: 1635 18.00 - 36.00: 208 36.00 - 54.00: 41 54.00 - 72.00: 8 72.00 - 90.00: 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: 166 0.054 - 0.081: 73 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 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. 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: 0.160 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: 1.320 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 0.091 3309 Z= 0.481 Angle : 0.991 25.902 4511 Z= 0.481 Chirality : 0.046 0.135 486 Planarity : 0.008 0.143 551 Dihedral : 16.507 89.997 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 : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1553 time to fit residues: 17.7330 Evaluate side-chains 66 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4934 ------------------------------------------------------------------------------- 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: 2.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3309 Z= 0.209 Angle : 0.683 7.169 4511 Z= 0.344 Chirality : 0.041 0.163 486 Planarity : 0.004 0.045 551 Dihedral : 8.167 83.362 434 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % 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: -2.60 (0.42), residues: 376 helix: -0.70 (0.33), residues: 243 sheet: None (None), residues: 0 loop : -3.67 (0.47), residues: 133 *********************** 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 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.1182 time to fit residues: 12.2936 Evaluate side-chains 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0344 time to fit residues: 0.6863 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 180 HIS R 211 GLN R 221 GLN ** 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: 0.7636 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3309 Z= 0.195 Angle : 0.626 6.363 4511 Z= 0.318 Chirality : 0.040 0.111 486 Planarity : 0.004 0.037 551 Dihedral : 7.898 77.515 434 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % 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: -1.85 (0.43), residues: 376 helix: -0.16 (0.34), residues: 244 sheet: None (None), residues: 0 loop : -3.32 (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 84 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 77 average time/residue: 0.1392 time to fit residues: 13.2149 Evaluate side-chains 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0392 time to fit residues: 0.8923 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 0.0010 chunk 32 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 overall best weight: 1.2190 ------------------------------------------------------------------------------- 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: 0.7573 moved from start: 0.2925 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= 0.159 Angle : 0.596 6.693 4511 Z= 0.297 Chirality : 0.039 0.113 486 Planarity : 0.004 0.053 551 Dihedral : 7.682 71.239 434 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -1.35 (0.44), residues: 376 helix: 0.17 (0.34), residues: 244 sheet: None (None), residues: 0 loop : -2.98 (0.52), 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 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 79 average time/residue: 0.1093 time to fit residues: 11.3049 Evaluate side-chains 71 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0412 time to fit residues: 0.7927 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3309 Z= 0.292 Angle : 0.679 6.254 4511 Z= 0.345 Chirality : 0.042 0.117 486 Planarity : 0.005 0.057 551 Dihedral : 7.887 68.744 434 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % 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: -1.36 (0.45), residues: 376 helix: 0.12 (0.34), residues: 244 sheet: None (None), residues: 0 loop : -2.89 (0.54), 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 77 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.1195 time to fit residues: 11.1310 Evaluate side-chains 65 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0317 time to fit residues: 0.7334 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7664 moved from start: 0.3231 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= 0.231 Angle : 0.649 6.560 4511 Z= 0.324 Chirality : 0.040 0.115 486 Planarity : 0.004 0.047 551 Dihedral : 7.691 72.072 434 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.30 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: -1.19 (0.45), residues: 376 helix: 0.26 (0.34), residues: 245 sheet: None (None), residues: 0 loop : -2.87 (0.54), 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 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.1183 time to fit residues: 10.6074 Evaluate side-chains 67 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0375 time to fit residues: 0.9113 ------------------------------------------------------------------------------- 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: 9.9990 chunk 36 optimal weight: 0.0770 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 24 optimal weight: 0.0020 overall best weight: 0.5146 ------------------------------------------------------------------------------- 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: 0.7544 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3309 Z= 0.155 Angle : 0.636 7.224 4511 Z= 0.308 Chirality : 0.040 0.129 486 Planarity : 0.004 0.043 551 Dihedral : 7.341 76.854 434 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.46), residues: 376 helix: 0.42 (0.35), residues: 248 sheet: -3.27 (1.81), residues: 12 loop : -2.65 (0.58), residues: 116 *********************** 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 80 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.1141 time to fit residues: 11.7808 Evaluate side-chains 70 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0316 time to fit residues: 0.6776 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3309 Z= 0.230 Angle : 0.653 7.663 4511 Z= 0.322 Chirality : 0.041 0.127 486 Planarity : 0.005 0.071 551 Dihedral : 7.329 72.414 434 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % 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: -0.98 (0.46), residues: 376 helix: 0.36 (0.34), residues: 248 sheet: -3.19 (1.81), residues: 12 loop : -2.55 (0.59), 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: 6 poor density : 69 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.1358 time to fit residues: 12.3950 Evaluate side-chains 68 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.450 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0430 time to fit residues: 0.9501 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 0.0470 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- 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: 0.7618 moved from start: 0.3950 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= 0.206 Angle : 0.662 7.800 4511 Z= 0.323 Chirality : 0.041 0.125 486 Planarity : 0.005 0.071 551 Dihedral : 7.300 70.050 434 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % 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: -0.94 (0.45), residues: 376 helix: 0.34 (0.34), residues: 247 sheet: -3.11 (1.85), residues: 12 loop : -2.37 (0.59), residues: 117 *********************** 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 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 0.1224 time to fit residues: 11.5196 Evaluate side-chains 69 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0347 time to fit residues: 0.7151 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 0.0470 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.4058 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= 0.198 Angle : 0.676 9.948 4511 Z= 0.326 Chirality : 0.042 0.277 486 Planarity : 0.005 0.071 551 Dihedral : 7.190 70.517 434 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % 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: -0.89 (0.46), residues: 376 helix: 0.37 (0.34), residues: 248 sheet: -3.00 (1.90), residues: 12 loop : -2.37 (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 68 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1257 time to fit residues: 10.9697 Evaluate side-chains 67 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4909 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.0570 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.129795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114419 restraints weight = 8483.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117710 restraints weight = 4285.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.119805 restraints weight = 2575.384| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3309 Z= 0.167 Angle : 0.657 9.101 4511 Z= 0.312 Chirality : 0.042 0.265 486 Planarity : 0.003 0.035 551 Dihedral : 6.953 73.718 434 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -0.81 (0.45), residues: 376 helix: 0.49 (0.34), residues: 244 sheet: -2.85 (1.90), residues: 12 loop : -2.41 (0.57), residues: 120 =============================================================================== Job complete usr+sys time: 919.67 seconds wall clock time: 17 minutes 37.59 seconds (1057.59 seconds total)