Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 19 23:36:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyj_21966/04_2023/6wyj_21966.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyj_21966/04_2023/6wyj_21966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyj_21966/04_2023/6wyj_21966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyj_21966/04_2023/6wyj_21966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyj_21966/04_2023/6wyj_21966.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyj_21966/04_2023/6wyj_21966.pdb" } resolution = 3.7 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 1942 2.51 5 N 465 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 394": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 2949 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2949 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain breaks: 2 Time building chain proxies: 2.12, per 1000 atoms: 0.72 Number of scatterers: 2949 At special positions: 0 Unit cell: (69.02, 70.006, 78.88, 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 18 16.00 O 524 8.00 N 465 7.00 C 1942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.35 Conformation dependent library (CDL) restraints added in 494.9 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.735A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 44 through 73 removed outlier: 4.195A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.565A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 108 removed outlier: 3.549A pdb=" N GLY A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.816A pdb=" N LEU A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.573A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 218 removed outlier: 3.560A pdb=" N ARG A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 225 through 255 removed outlier: 3.585A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.590A pdb=" N LYS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.729A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.507A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.087A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.639A pdb=" N ALA A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.814A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.714A pdb=" N ALA A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 690 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: 0.77 Time building geometry restraints manager: 1.44 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: 907 1.34 - 1.46: 524 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2997 Sorted by residual: bond pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.35e-02 5.49e+03 8.99e+00 bond pdb=" CA MET A 311 " pdb=" CB MET A 311 " ideal model delta sigma weight residual 1.531 1.467 0.064 3.28e-02 9.30e+02 3.77e+00 bond pdb=" CB THR A 154 " pdb=" CG2 THR A 154 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB THR A 275 " pdb=" CG2 THR A 275 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.54e+00 bond pdb=" CG LEU A 190 " pdb=" CD1 LEU A 190 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.37e+00 ... (remaining 2992 not shown) Histogram of bond angle deviations from ideal: 98.41 - 104.98: 59 104.98 - 111.54: 1484 111.54 - 118.10: 867 118.10 - 124.66: 1643 124.66 - 131.22: 25 Bond angle restraints: 4078 Sorted by residual: angle pdb=" C ASN A 173 " pdb=" N GLU A 174 " pdb=" CA GLU A 174 " ideal model delta sigma weight residual 120.99 125.55 -4.56 1.86e+00 2.89e-01 6.00e+00 angle pdb=" N PRO A 356 " pdb=" CA PRO A 356 " pdb=" C PRO A 356 " ideal model delta sigma weight residual 112.47 117.44 -4.97 2.06e+00 2.36e-01 5.81e+00 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 118.19 -4.29 1.80e+00 3.09e-01 5.68e+00 angle pdb=" C ALA A 205 " pdb=" CA ALA A 205 " pdb=" CB ALA A 205 " ideal model delta sigma weight residual 113.49 109.32 4.17 1.82e+00 3.02e-01 5.26e+00 angle pdb=" CA ALA A 205 " pdb=" C ALA A 205 " pdb=" N PRO A 206 " ideal model delta sigma weight residual 120.52 118.83 1.69 8.30e-01 1.45e+00 4.13e+00 ... (remaining 4073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1653 17.19 - 34.37: 107 34.37 - 51.56: 15 51.56 - 68.74: 3 68.74 - 85.93: 3 Dihedral angle restraints: 1781 sinusoidal: 649 harmonic: 1132 Sorted by residual: dihedral pdb=" CA VAL A 355 " pdb=" C VAL A 355 " pdb=" N PRO A 356 " pdb=" CA PRO A 356 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR A 352 " pdb=" C THR A 352 " pdb=" N ALA A 353 " pdb=" CA ALA A 353 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 37 " pdb=" CB ASP A 37 " pdb=" CG ASP A 37 " pdb=" OD1 ASP A 37 " ideal model delta sinusoidal sigma weight residual -30.00 -89.49 59.49 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 1778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 271 0.035 - 0.069: 173 0.069 - 0.104: 64 0.104 - 0.139: 8 0.139 - 0.173: 4 Chirality restraints: 520 Sorted by residual: chirality pdb=" CA PRO A 356 " pdb=" N PRO A 356 " pdb=" C PRO A 356 " pdb=" CB PRO A 356 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" C PRO A 60 " pdb=" CB PRO A 60 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CB ILE A 411 " pdb=" CA ILE A 411 " pdb=" CG1 ILE A 411 " pdb=" CG2 ILE A 411 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 517 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 206 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.010 2.00e-02 2.50e+03 6.87e-03 9.43e-01 pdb=" CG TYR A 299 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 59 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.33e-01 pdb=" N PRO A 60 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.013 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 840 2.79 - 3.32: 3220 3.32 - 3.85: 4503 3.85 - 4.37: 5358 4.37 - 4.90: 8867 Nonbonded interactions: 22788 Sorted by model distance: nonbonded pdb=" O SER A 179 " pdb=" OG1 THR A 182 " model vdw 2.268 2.440 nonbonded pdb=" O GLU A 172 " pdb=" NH2 ARG A 177 " model vdw 2.322 2.520 nonbonded pdb=" O LEU A 282 " pdb=" OG1 THR A 285 " model vdw 2.328 2.440 nonbonded pdb=" O THR A 271 " pdb=" OG1 THR A 275 " model vdw 2.377 2.440 nonbonded pdb=" O ILE A 187 " pdb=" N LEU A 190 " model vdw 2.422 2.520 ... (remaining 22783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.540 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.040 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.010 0.064 2997 Z= 0.632 Angle : 0.644 4.965 4078 Z= 0.351 Chirality : 0.049 0.173 520 Planarity : 0.003 0.030 496 Dihedral : 12.333 85.929 1061 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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: -4.80 (0.30), residues: 393 helix: -2.79 (0.21), residues: 301 sheet: None (None), residues: 0 loop : -3.77 (0.47), residues: 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1706 time to fit residues: 6.9105 Evaluate side-chains 29 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 2997 Z= 0.227 Angle : 0.572 5.335 4078 Z= 0.308 Chirality : 0.042 0.168 520 Planarity : 0.004 0.036 496 Dihedral : 4.574 33.570 421 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.64 % 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: -0.18 (0.39), residues: 393 helix: 0.39 (0.27), residues: 324 sheet: None (None), residues: 0 loop : -2.19 (0.67), residues: 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.351 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.1340 time to fit residues: 6.3620 Evaluate side-chains 33 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 2997 Z= 0.234 Angle : 0.551 5.338 4078 Z= 0.291 Chirality : 0.042 0.186 520 Planarity : 0.004 0.035 496 Dihedral : 4.206 28.099 421 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.28 % 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: 1.24 (0.41), residues: 393 helix: 1.46 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.93 (0.62), residues: 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.339 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1369 time to fit residues: 8.1561 Evaluate side-chains 44 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0615 time to fit residues: 0.7312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2997 Z= 0.248 Angle : 0.564 5.341 4078 Z= 0.292 Chirality : 0.044 0.377 520 Planarity : 0.004 0.034 496 Dihedral : 4.173 25.783 421 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.60 % 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: 1.41 (0.41), residues: 393 helix: 1.53 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.64 (0.65), residues: 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.298 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1245 time to fit residues: 7.9074 Evaluate side-chains 44 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0307 time to fit residues: 0.6334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.0050 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3404 ------------------------------------------------------------------------------- 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: 0.7473 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2997 Z= 0.176 Angle : 0.497 5.322 4078 Z= 0.257 Chirality : 0.039 0.171 520 Planarity : 0.004 0.033 496 Dihedral : 3.973 26.766 421 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.32 % 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: 1.82 (0.42), residues: 393 helix: 1.79 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.59 (0.66), residues: 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.343 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1467 time to fit residues: 8.1690 Evaluate side-chains 38 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 2997 Z= 0.232 Angle : 0.555 6.034 4078 Z= 0.284 Chirality : 0.044 0.381 520 Planarity : 0.004 0.033 496 Dihedral : 3.987 24.916 421 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.96 % 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: 1.76 (0.41), residues: 393 helix: 1.74 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.32 (0.68), residues: 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.286 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.1284 time to fit residues: 6.3232 Evaluate side-chains 37 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0515 time to fit residues: 0.4670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7522 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2997 Z= 0.215 Angle : 0.530 5.350 4078 Z= 0.273 Chirality : 0.042 0.303 520 Planarity : 0.004 0.032 496 Dihedral : 3.915 23.420 421 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 1.92 % 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: 1.86 (0.41), residues: 393 helix: 1.76 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.15 (0.68), residues: 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.368 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.1385 time to fit residues: 8.1003 Evaluate side-chains 39 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0319 time to fit residues: 0.5786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 2997 Z= 0.270 Angle : 0.565 5.397 4078 Z= 0.291 Chirality : 0.042 0.169 520 Planarity : 0.004 0.031 496 Dihedral : 3.973 20.581 421 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 1.28 % 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: 1.54 (0.41), residues: 393 helix: 1.53 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.21 (0.67), residues: 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.311 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1434 time to fit residues: 7.4653 Evaluate side-chains 36 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0340 time to fit residues: 0.6039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7518 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 2997 Z= 0.189 Angle : 0.512 5.271 4078 Z= 0.262 Chirality : 0.040 0.191 520 Planarity : 0.004 0.031 496 Dihedral : 3.830 21.389 421 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 0.64 % 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: 1.84 (0.42), residues: 393 helix: 1.78 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.32 (0.65), residues: 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.334 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 0.1212 time to fit residues: 6.2424 Evaluate side-chains 35 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2997 Z= 0.229 Angle : 0.549 5.336 4078 Z= 0.285 Chirality : 0.042 0.240 520 Planarity : 0.004 0.030 496 Dihedral : 3.866 20.392 421 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 1.73 (0.41), residues: 393 helix: 1.71 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.39 (0.64), residues: 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.356 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1323 time to fit residues: 5.9446 Evaluate side-chains 34 residues out of total 313 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.0030 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.164144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.150236 restraints weight = 3343.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.147205 restraints weight = 5480.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 102)---------------| | r_work = 0.3452 r_free = 0.3452 target = 0.141927 restraints weight = 5287.807| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 2997 Z= 0.164 Angle : 0.500 5.288 4078 Z= 0.257 Chirality : 0.040 0.216 520 Planarity : 0.004 0.034 496 Dihedral : 3.680 21.175 421 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 2.16 (0.42), residues: 393 helix: 1.98 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -1.36 (0.65), residues: 66 =============================================================================== Job complete usr+sys time: 944.15 seconds wall clock time: 17 minutes 40.14 seconds (1060.14 seconds total)