Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:52:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knt_22962/11_2022/7knt_22962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knt_22962/11_2022/7knt_22962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knt_22962/11_2022/7knt_22962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knt_22962/11_2022/7knt_22962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knt_22962/11_2022/7knt_22962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knt_22962/11_2022/7knt_22962.pdb" } resolution = 3.15 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= -0.000 sd= 0.037 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 None 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: 3716 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 920 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2796 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 4 Time building chain proxies: 2.63, per 1000 atoms: 0.71 Number of scatterers: 3716 At special positions: 0 Unit cell: (74.7, 97.94, 92.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 628 8.00 N 614 7.00 C 2443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " 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 672.8 milliseconds 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 73.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.797A pdb=" N CYS E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 removed outlier: 5.862A pdb=" N GLU E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU E 55 " --> pdb=" O VAL E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 81 Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.899A pdb=" N ARG E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 100 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 142 removed outlier: 3.670A pdb=" N PHE E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.740A pdb=" N VAL E 138 " --> pdb=" O THR E 134 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 54 removed outlier: 3.671A pdb=" N ASN R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 128 removed outlier: 3.679A pdb=" N CYS R 127 " --> pdb=" O TYR R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 147 removed outlier: 4.086A pdb=" N LYS R 136 " --> pdb=" O HIS R 132 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 166 removed outlier: 3.763A pdb=" N SER R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE R 153 " --> pdb=" O HIS R 149 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 198 removed outlier: 3.540A pdb=" N ASN R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE R 182 " --> pdb=" O LYS R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.633A pdb=" N VAL R 205 " --> pdb=" O ASN R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.882A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY R 234 " --> pdb=" O MET R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 261 removed outlier: 3.517A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.575A pdb=" N ALA R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.619A pdb=" N ILE R 284 " --> pdb=" O ASN R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 319 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 340 removed outlier: 3.523A pdb=" N VAL R 335 " --> pdb=" O TYR R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 351 removed outlier: 3.736A pdb=" N LEU R 344 " --> pdb=" O ILE R 340 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU R 348 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 375 removed outlier: 3.516A pdb=" N HIS R 374 " --> pdb=" O HIS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 385 removed outlier: 3.642A pdb=" N LEU R 379 " --> pdb=" O PHE R 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 397 Processing sheet with id=AA1, first strand: chain 'R' and resid 86 through 87 removed outlier: 4.049A pdb=" N GLN R 86 " --> pdb=" O VAL R 101 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 612 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: 0.88 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1133 1.35 - 1.47: 1021 1.47 - 1.59: 1627 1.59 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 3823 Sorted by residual: bond pdb=" N VAL R 214 " pdb=" CA VAL R 214 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.53e+00 bond pdb=" N ILE R 293 " pdb=" CA ILE R 293 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.06e-02 8.90e+03 8.28e+00 bond pdb=" N ASP R 280 " pdb=" CA ASP R 280 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.27e-02 6.20e+03 7.30e+00 bond pdb=" N ARG R 274 " pdb=" CA ARG R 274 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.37e+00 bond pdb=" N TYR R 277 " pdb=" CA TYR R 277 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.31e+00 ... (remaining 3818 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.42: 99 106.42 - 113.37: 2050 113.37 - 120.33: 1493 120.33 - 127.28: 1504 127.28 - 134.24: 61 Bond angle restraints: 5207 Sorted by residual: angle pdb=" CA LEU E 55 " pdb=" CB LEU E 55 " pdb=" CG LEU E 55 " ideal model delta sigma weight residual 116.30 130.84 -14.54 3.50e+00 8.16e-02 1.73e+01 angle pdb=" N ILE R 293 " pdb=" CA ILE R 293 " pdb=" C ILE R 293 " ideal model delta sigma weight residual 112.98 108.22 4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" N HIS R 289 " pdb=" CA HIS R 289 " pdb=" C HIS R 289 " ideal model delta sigma weight residual 113.01 108.50 4.51 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA ASN R 279 " pdb=" C ASN R 279 " pdb=" O ASN R 279 " ideal model delta sigma weight residual 122.37 118.10 4.27 1.15e+00 7.56e-01 1.38e+01 angle pdb=" N TRP R 283 " pdb=" CA TRP R 283 " pdb=" C TRP R 283 " ideal model delta sigma weight residual 112.86 108.76 4.10 1.22e+00 6.72e-01 1.13e+01 ... (remaining 5202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 1888 14.14 - 28.28: 219 28.28 - 42.42: 76 42.42 - 56.56: 15 56.56 - 70.70: 11 Dihedral angle restraints: 2209 sinusoidal: 869 harmonic: 1340 Sorted by residual: dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 32.21 60.79 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -42.02 -43.98 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 74 " pdb=" CB CYS R 74 " ideal model delta sinusoidal sigma weight residual 93.00 51.75 41.25 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 2206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 420 0.043 - 0.087: 133 0.087 - 0.130: 21 0.130 - 0.174: 5 0.174 - 0.217: 6 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA THR R 288 " pdb=" N THR R 288 " pdb=" C THR R 288 " pdb=" CB THR R 288 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR R 292 " pdb=" N TYR R 292 " pdb=" C TYR R 292 " pdb=" CB TYR R 292 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE R 293 " pdb=" CA ILE R 293 " pdb=" CG1 ILE R 293 " pdb=" CG2 ILE R 293 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 582 not shown) Planarity restraints: 637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 276 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LEU R 276 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU R 276 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR R 277 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 399 " 0.016 2.00e-02 2.50e+03 1.43e-02 5.10e+00 pdb=" CG TRP R 399 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP R 399 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP R 399 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 399 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 399 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 399 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 399 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 399 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 399 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 296 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO R 297 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 297 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 297 " -0.031 5.00e-02 4.00e+02 ... (remaining 634 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 51 2.67 - 3.23: 3786 3.23 - 3.79: 5929 3.79 - 4.34: 8015 4.34 - 4.90: 12381 Nonbonded interactions: 30162 Sorted by model distance: nonbonded pdb=" OD2 ASP E 47 " pdb=" OG SER E 65 " model vdw 2.116 2.440 nonbonded pdb=" OD2 ASP R 96 " pdb=" OG SER R 98 " model vdw 2.257 2.440 nonbonded pdb=" O TYR R 46 " pdb=" NE2 GLN R 50 " model vdw 2.278 2.520 nonbonded pdb=" O ALA E 70 " pdb=" OG1 THR E 73 " model vdw 2.353 2.440 nonbonded pdb=" OD2 ASP R 70 " pdb=" OH TYR R 124 " model vdw 2.381 2.440 ... (remaining 30157 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2443 2.51 5 N 614 2.21 5 O 628 1.98 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 3.050 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3823 Z= 0.246 Angle : 0.753 14.540 5207 Z= 0.458 Chirality : 0.045 0.217 585 Planarity : 0.004 0.056 637 Dihedral : 14.556 70.696 1323 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.48 (0.40), residues: 443 helix: 0.22 (0.32), residues: 287 sheet: -0.67 (1.82), residues: 12 loop : -1.22 (0.50), residues: 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.351 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.1354 time to fit residues: 11.7409 Evaluate side-chains 56 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0300 time to fit residues: 0.4687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 187 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3823 Z= 0.215 Angle : 0.672 13.398 5207 Z= 0.345 Chirality : 0.042 0.163 585 Planarity : 0.005 0.041 637 Dihedral : 4.691 17.928 491 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.10 (0.40), residues: 443 helix: 0.41 (0.30), residues: 293 sheet: -0.62 (1.79), residues: 12 loop : -0.84 (0.55), residues: 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.372 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 72 average time/residue: 0.1868 time to fit residues: 16.2974 Evaluate side-chains 60 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0426 time to fit residues: 1.2900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 27 optimal weight: 0.0170 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 39 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3823 Z= 0.174 Angle : 0.645 14.168 5207 Z= 0.316 Chirality : 0.040 0.131 585 Planarity : 0.005 0.044 637 Dihedral : 4.496 16.994 491 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.07 (0.40), residues: 443 helix: 0.58 (0.30), residues: 298 sheet: -0.36 (1.83), residues: 12 loop : -0.95 (0.55), residues: 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.445 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.1804 time to fit residues: 13.6032 Evaluate side-chains 55 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1226 time to fit residues: 0.9780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 39 ASN R 226 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3823 Z= 0.199 Angle : 0.611 12.026 5207 Z= 0.307 Chirality : 0.040 0.120 585 Planarity : 0.004 0.041 637 Dihedral : 4.468 17.243 491 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.21 (0.40), residues: 443 helix: 0.73 (0.30), residues: 296 sheet: -0.25 (1.86), residues: 12 loop : -0.99 (0.55), residues: 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.419 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 59 average time/residue: 0.1905 time to fit residues: 13.8038 Evaluate side-chains 56 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0412 time to fit residues: 0.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN ** R 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 3823 Z= 0.222 Angle : 0.606 10.571 5207 Z= 0.308 Chirality : 0.041 0.165 585 Planarity : 0.004 0.039 637 Dihedral : 4.446 16.021 491 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.27 (0.41), residues: 443 helix: 0.77 (0.30), residues: 299 sheet: -0.18 (1.84), residues: 12 loop : -1.01 (0.55), residues: 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.430 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 68 average time/residue: 0.1635 time to fit residues: 13.8154 Evaluate side-chains 57 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0425 time to fit residues: 1.0019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN R 279 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3823 Z= 0.199 Angle : 0.639 14.431 5207 Z= 0.312 Chirality : 0.041 0.112 585 Planarity : 0.004 0.039 637 Dihedral : 4.423 15.989 491 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.29 (0.40), residues: 443 helix: 0.79 (0.30), residues: 299 sheet: -0.10 (1.83), residues: 12 loop : -1.01 (0.55), residues: 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.447 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 60 average time/residue: 0.1580 time to fit residues: 11.9317 Evaluate side-chains 56 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0375 time to fit residues: 0.8509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3823 Z= 0.182 Angle : 0.633 13.787 5207 Z= 0.309 Chirality : 0.040 0.146 585 Planarity : 0.004 0.040 637 Dihedral : 4.398 16.323 491 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.35 (0.40), residues: 443 helix: 0.88 (0.30), residues: 299 sheet: -0.02 (1.86), residues: 12 loop : -1.13 (0.54), residues: 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.433 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.1813 time to fit residues: 13.2367 Evaluate side-chains 53 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0479 time to fit residues: 0.8271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3823 Z= 0.180 Angle : 0.647 12.499 5207 Z= 0.312 Chirality : 0.040 0.146 585 Planarity : 0.004 0.040 637 Dihedral : 4.458 21.814 491 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.40), residues: 443 helix: 0.97 (0.30), residues: 299 sheet: 0.29 (1.84), residues: 12 loop : -1.25 (0.53), residues: 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.453 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.2095 time to fit residues: 14.9447 Evaluate side-chains 56 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0317 time to fit residues: 0.6711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3823 Z= 0.170 Angle : 0.662 12.822 5207 Z= 0.317 Chirality : 0.040 0.115 585 Planarity : 0.004 0.041 637 Dihedral : 4.383 19.774 491 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.49 (0.40), residues: 443 helix: 1.07 (0.30), residues: 299 sheet: 0.23 (1.83), residues: 12 loop : -1.32 (0.53), residues: 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.390 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 0.1729 time to fit residues: 12.0255 Evaluate side-chains 58 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0431 time to fit residues: 0.8531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3823 Z= 0.229 Angle : 0.686 12.646 5207 Z= 0.333 Chirality : 0.041 0.117 585 Planarity : 0.004 0.037 637 Dihedral : 4.425 20.201 491 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.39 (0.40), residues: 443 helix: 0.98 (0.30), residues: 299 sheet: 0.13 (1.77), residues: 12 loop : -1.33 (0.53), residues: 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 886 Ramachandran restraints generated. 443 Oldfield, 0 Emsley, 443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.442 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.1824 time to fit residues: 12.9712 Evaluate side-chains 59 residues out of total 405 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0450 time to fit residues: 0.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.0470 chunk 27 optimal weight: 0.0970 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.114361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.089152 restraints weight = 9555.793| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.48 r_work: 0.3734 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work: 0.3718 rms_B_bonded: 3.26 restraints_weight: 0.1250 r_work: 0.3710 rms_B_bonded: 3.30 restraints_weight: 0.0625 r_work: 0.3701 rms_B_bonded: 3.36 restraints_weight: 0.0312 r_work: 0.3693 rms_B_bonded: 3.44 restraints_weight: 0.0156 r_work: 0.3684 rms_B_bonded: 3.54 restraints_weight: 0.0078 r_work: 0.3675 rms_B_bonded: 3.65 restraints_weight: 0.0039 r_work: 0.3666 rms_B_bonded: 3.77 restraints_weight: 0.0020 r_work: 0.3657 rms_B_bonded: 3.92 restraints_weight: 0.0010 r_work: 0.3647 rms_B_bonded: 4.07 restraints_weight: 0.0005 r_work: 0.3637 rms_B_bonded: 4.25 restraints_weight: 0.0002 r_work: 0.3627 rms_B_bonded: 4.44 restraints_weight: 0.0001 r_work: 0.3617 rms_B_bonded: 4.64 restraints_weight: 0.0001 r_work: 0.3606 rms_B_bonded: 4.87 restraints_weight: 0.0000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3823 Z= 0.165 Angle : 0.661 12.755 5207 Z= 0.315 Chirality : 0.040 0.114 585 Planarity : 0.004 0.042 637 Dihedral : 4.325 19.556 491 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.41), residues: 443 helix: 1.16 (0.31), residues: 299 sheet: 0.20 (1.79), residues: 12 loop : -1.37 (0.53), residues: 132 =============================================================================== Job complete usr+sys time: 1175.41 seconds wall clock time: 22 minutes 17.29 seconds (1337.29 seconds total)