Starting phenix.real_space_refine on Wed Mar 5 18:49:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jnc_9847/03_2025/6jnc_9847.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnc_9847/03_2025/6jnc_9847.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/cci-nas-00/data/ceres_data/6jnc_9847/03_2025/6jnc_9847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2025/6jnc_9847.map" model { file = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2025/6jnc_9847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2025/6jnc_9847.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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 15 5.16 5 C 2103 2.51 5 N 561 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3294 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3286 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'TRS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.87 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.34, 75.69, 74.82, 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 15 16.00 O 615 8.00 N 561 7.00 C 2103 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 - 3.00 Amino acid : True - 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: 0.80 Conformation dependent library (CDL) restraints added in 412.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 3 sheets defined 49.9% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.565A pdb=" N MET A 9 " --> pdb=" O ASP A 5 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 13 " --> pdb=" O MET A 9 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.760A pdb=" N GLU A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.902A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.554A pdb=" N LEU A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.834A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.545A pdb=" N ILE A 135 " --> pdb=" O TYR A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 removed outlier: 3.796A pdb=" N TRP A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.726A pdb=" N VAL A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.805A pdb=" N ILE A 181 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 189 through 207 removed outlier: 3.982A pdb=" N ALA A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 234 removed outlier: 4.276A pdb=" N TYR A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 removed outlier: 4.105A pdb=" N LEU A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.549A pdb=" N LEU A 284 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 removed outlier: 3.961A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.905A pdb=" N ASN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.542A pdb=" N SER A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.560A pdb=" N GLN A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 392 removed outlier: 3.534A pdb=" N LYS A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 414 removed outlier: 3.575A pdb=" N TYR A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 3.521A pdb=" N ARG A 36 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45 removed outlier: 3.521A pdb=" N ARG A 36 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 55 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 242 removed outlier: 6.425A pdb=" N ILE A 215 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL A 314 " --> pdb=" O ILE A 338 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 384 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: 0.90 Time building geometry restraints manager: 0.97 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: 1061 1.34 - 1.45: 435 1.45 - 1.57: 1841 1.57 - 1.69: 0 1.69 - 1.80: 29 Bond restraints: 3366 Sorted by residual: bond pdb=" CA PHE A 341 " pdb=" C PHE A 341 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.48e-02 4.57e+03 1.45e+01 bond pdb=" N TRS A 901 " pdb=" C TRS A 901 " ideal model delta sigma weight residual 1.501 1.462 0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" CB VAL A 356 " pdb=" CG2 VAL A 356 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB TRP A 382 " pdb=" CG TRP A 382 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.49e+00 bond pdb=" C PHE A 341 " pdb=" N LEU A 342 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.42e-02 4.96e+03 1.96e+00 ... (remaining 3361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 4216 1.55 - 3.11: 312 3.11 - 4.66: 26 4.66 - 6.22: 7 6.22 - 7.77: 1 Bond angle restraints: 4562 Sorted by residual: angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 113.20 107.26 5.94 9.60e-01 1.09e+00 3.83e+01 angle pdb=" C ASP A 340 " pdb=" N PHE A 341 " pdb=" CA PHE A 341 " ideal model delta sigma weight residual 122.65 114.88 7.77 1.60e+00 3.91e-01 2.36e+01 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.17 108.44 3.73 9.50e-01 1.11e+00 1.54e+01 angle pdb=" C LYS A 271 " pdb=" N ASP A 272 " pdb=" CA ASP A 272 " ideal model delta sigma weight residual 122.19 127.16 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 128.57 -5.52 1.57e+00 4.06e-01 1.24e+01 ... (remaining 4557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 1792 16.63 - 33.27: 164 33.27 - 49.90: 47 49.90 - 66.53: 11 66.53 - 83.17: 2 Dihedral angle restraints: 2016 sinusoidal: 818 harmonic: 1198 Sorted by residual: dihedral pdb=" CA TRP A 382 " pdb=" C TRP A 382 " pdb=" N GLU A 383 " pdb=" CA GLU A 383 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " pdb=" OD1 ASP A 290 " ideal model delta sinusoidal sigma weight residual -30.00 -90.08 60.08 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA TYR A 147 " pdb=" C TYR A 147 " pdb=" N THR A 148 " pdb=" CA THR A 148 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 259 0.035 - 0.070: 161 0.070 - 0.105: 48 0.105 - 0.139: 22 0.139 - 0.174: 7 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB ILE A 23 " pdb=" CA ILE A 23 " pdb=" CG1 ILE A 23 " pdb=" CG2 ILE A 23 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA PHE A 341 " pdb=" N PHE A 341 " pdb=" C PHE A 341 " pdb=" CB PHE A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA TYR A 147 " pdb=" N TYR A 147 " pdb=" C TYR A 147 " pdb=" CB TYR A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 494 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.044 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO A 150 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 142 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 99 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO A 100 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " 0.033 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1076 2.82 - 3.34: 2645 3.34 - 3.86: 5053 3.86 - 4.38: 5963 4.38 - 4.90: 10428 Nonbonded interactions: 25165 Sorted by model distance: nonbonded pdb=" N ASP A 340 " pdb=" OD1 ASP A 340 " model vdw 2.304 3.120 nonbonded pdb=" OD2 ASP A 145 " pdb=" O2 TRS A 901 " model vdw 2.368 3.040 nonbonded pdb=" N ASP A 256 " pdb=" OD1 ASP A 256 " model vdw 2.370 3.120 nonbonded pdb=" O PHE A 353 " pdb=" NE2 GLN A 357 " model vdw 2.372 3.120 nonbonded pdb=" N ASN A 149 " pdb=" OD1 ASN A 149 " model vdw 2.377 3.120 ... (remaining 25160 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.009 0.062 3366 Z= 0.561 Angle : 0.872 7.773 4562 Z= 0.560 Chirality : 0.052 0.174 497 Planarity : 0.008 0.065 584 Dihedral : 14.724 83.169 1252 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 9.09 % Allowed : 10.85 % Favored : 80.06 % 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: -5.69 (0.30), residues: 417 helix: -4.85 (0.13), residues: 188 sheet: -1.75 (0.68), residues: 61 loop : -2.99 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 30 HIS 0.006 0.001 HIS A 388 PHE 0.011 0.002 PHE A 57 TYR 0.012 0.002 TYR A 363 ARG 0.003 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 5 ASP cc_start: 0.7896 (t70) cc_final: 0.7309 (t0) REVERT: A 48 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7689 (p0) REVERT: A 180 SER cc_start: 0.8179 (p) cc_final: 0.7593 (m) REVERT: A 246 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5805 (ttt90) REVERT: A 269 SER cc_start: 0.7051 (t) cc_final: 0.6632 (p) outliers start: 31 outliers final: 5 residues processed: 105 average time/residue: 0.1867 time to fit residues: 23.1519 Evaluate side-chains 59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.0030 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 386 ASN A 394 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097387 restraints weight = 5020.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098051 restraints weight = 3783.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098791 restraints weight = 3461.154| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3366 Z= 0.153 Angle : 0.531 6.489 4562 Z= 0.287 Chirality : 0.045 0.172 497 Planarity : 0.006 0.044 584 Dihedral : 7.306 55.922 474 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.28 % Allowed : 15.54 % Favored : 79.18 % 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: -3.91 (0.34), residues: 417 helix: -2.86 (0.28), residues: 193 sheet: -1.67 (0.64), residues: 56 loop : -2.37 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.001 0.000 HIS A 75 PHE 0.008 0.001 PHE A 197 TYR 0.033 0.001 TYR A 225 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7375 (ttmt) REVERT: A 91 THR cc_start: 0.8674 (t) cc_final: 0.8381 (m) REVERT: A 180 SER cc_start: 0.7853 (p) cc_final: 0.7416 (m) REVERT: A 246 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5493 (ttt90) REVERT: A 331 ARG cc_start: 0.7394 (tmm-80) cc_final: 0.6981 (ptm-80) REVERT: A 400 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5859 (t80) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 0.1575 time to fit residues: 13.6819 Evaluate side-chains 56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.0170 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098286 restraints weight = 4977.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098261 restraints weight = 4053.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098782 restraints weight = 3787.584| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3366 Z= 0.174 Angle : 0.504 5.655 4562 Z= 0.271 Chirality : 0.046 0.139 497 Planarity : 0.005 0.036 584 Dihedral : 6.225 44.222 471 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.23 % Allowed : 21.11 % Favored : 75.66 % 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: -2.92 (0.37), residues: 417 helix: -1.77 (0.33), residues: 196 sheet: -1.46 (0.63), residues: 60 loop : -2.12 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.003 0.001 HIS A 267 PHE 0.007 0.001 PHE A 7 TYR 0.029 0.001 TYR A 225 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.364 Fit side-chains REVERT: A 69 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8024 (ttmt) REVERT: A 180 SER cc_start: 0.8305 (p) cc_final: 0.7917 (m) REVERT: A 246 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5597 (ttt90) REVERT: A 269 SER cc_start: 0.7737 (t) cc_final: 0.7515 (p) REVERT: A 419 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7523 (mtpp) outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.1472 time to fit residues: 11.2005 Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 340 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092346 restraints weight = 5235.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.093377 restraints weight = 4263.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.093580 restraints weight = 3994.781| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3366 Z= 0.323 Angle : 0.594 7.060 4562 Z= 0.315 Chirality : 0.049 0.158 497 Planarity : 0.005 0.036 584 Dihedral : 6.491 50.618 469 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.81 % Allowed : 21.70 % Favored : 74.49 % 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: -2.64 (0.38), residues: 417 helix: -1.54 (0.34), residues: 196 sheet: -1.16 (0.69), residues: 60 loop : -2.07 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.024 0.001 TYR A 225 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.394 Fit side-chains REVERT: A 69 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8236 (ttmt) REVERT: A 246 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6144 (ttt90) outliers start: 13 outliers final: 7 residues processed: 45 average time/residue: 0.1846 time to fit residues: 10.1833 Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.094701 restraints weight = 5142.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095081 restraints weight = 4091.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095229 restraints weight = 4097.331| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3366 Z= 0.176 Angle : 0.470 4.421 4562 Z= 0.253 Chirality : 0.045 0.130 497 Planarity : 0.004 0.032 584 Dihedral : 6.059 49.744 469 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.52 % Allowed : 21.11 % Favored : 75.37 % 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: -2.15 (0.39), residues: 417 helix: -1.04 (0.36), residues: 196 sheet: -1.00 (0.69), residues: 60 loop : -1.91 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.027 0.001 TYR A 225 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.397 Fit side-chains REVERT: A 69 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8196 (ttmt) REVERT: A 218 GLN cc_start: 0.8270 (tt0) cc_final: 0.7967 (tp40) REVERT: A 408 TYR cc_start: 0.8569 (t80) cc_final: 0.8353 (t80) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.1547 time to fit residues: 9.0192 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.090634 restraints weight = 5327.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.091133 restraints weight = 4332.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.091212 restraints weight = 4301.439| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3366 Z= 0.311 Angle : 0.558 5.119 4562 Z= 0.293 Chirality : 0.048 0.162 497 Planarity : 0.004 0.033 584 Dihedral : 6.299 49.586 465 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.23 % Allowed : 22.29 % Favored : 74.49 % 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: -2.11 (0.39), residues: 417 helix: -0.97 (0.37), residues: 196 sheet: -1.08 (0.71), residues: 58 loop : -1.90 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.014 0.002 TYR A 225 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.378 Fit side-chains REVERT: A 69 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8305 (ttmt) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.1514 time to fit residues: 8.7104 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.6562 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.122063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.096223 restraints weight = 5057.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.096204 restraints weight = 4483.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.096372 restraints weight = 3886.075| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.7566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3366 Z= 0.131 Angle : 0.452 4.056 4562 Z= 0.241 Chirality : 0.044 0.139 497 Planarity : 0.004 0.030 584 Dihedral : 5.528 48.888 463 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.05 % Allowed : 22.58 % Favored : 75.37 % 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: -1.68 (0.40), residues: 417 helix: -0.53 (0.38), residues: 196 sheet: -0.95 (0.70), residues: 60 loop : -1.78 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 92 HIS 0.003 0.001 HIS A 388 PHE 0.006 0.001 PHE A 381 TYR 0.019 0.001 TYR A 225 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.355 Fit side-chains REVERT: A 69 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8013 (ttmt) REVERT: A 262 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7539 (mtmt) REVERT: A 279 ILE cc_start: 0.7640 (mm) cc_final: 0.7257 (pt) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.1694 time to fit residues: 8.8119 Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.091338 restraints weight = 5155.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.092339 restraints weight = 4281.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092853 restraints weight = 4135.897| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3366 Z= 0.316 Angle : 0.600 7.676 4562 Z= 0.307 Chirality : 0.048 0.169 497 Planarity : 0.004 0.033 584 Dihedral : 6.132 58.346 463 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.23 % Allowed : 22.29 % Favored : 74.49 % 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: -1.65 (0.41), residues: 417 helix: -0.56 (0.38), residues: 197 sheet: -0.99 (0.69), residues: 60 loop : -1.65 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.018 0.002 TYR A 225 ARG 0.002 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.400 Fit side-chains REVERT: A 69 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8296 (ttmt) REVERT: A 262 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7603 (mtmt) outliers start: 11 outliers final: 8 residues processed: 45 average time/residue: 0.1567 time to fit residues: 8.9089 Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.120417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.093956 restraints weight = 5177.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.095405 restraints weight = 4499.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.095609 restraints weight = 4222.657| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.7775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3366 Z= 0.173 Angle : 0.499 5.645 4562 Z= 0.259 Chirality : 0.045 0.132 497 Planarity : 0.004 0.032 584 Dihedral : 5.536 49.060 463 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.05 % Allowed : 24.05 % Favored : 73.90 % 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: -1.39 (0.41), residues: 417 helix: -0.27 (0.39), residues: 197 sheet: -0.98 (0.69), residues: 60 loop : -1.59 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.004 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.020 0.001 TYR A 225 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.412 Fit side-chains REVERT: A 69 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8119 (ttmt) REVERT: A 262 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7602 (mtmt) REVERT: A 279 ILE cc_start: 0.7738 (mm) cc_final: 0.7336 (pt) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.1636 time to fit residues: 8.9376 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.121283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.095153 restraints weight = 5043.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095201 restraints weight = 4950.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.095396 restraints weight = 4117.210| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3366 Z= 0.145 Angle : 0.488 5.845 4562 Z= 0.253 Chirality : 0.044 0.131 497 Planarity : 0.004 0.031 584 Dihedral : 5.231 49.210 463 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 23.75 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.41), residues: 417 helix: -0.06 (0.39), residues: 197 sheet: -0.89 (0.69), residues: 60 loop : -1.56 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.003 0.001 HIS A 388 PHE 0.005 0.001 PHE A 381 TYR 0.021 0.001 TYR A 225 ARG 0.001 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.371 Fit side-chains REVERT: A 69 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: A 237 MET cc_start: 0.6387 (mmt) cc_final: 0.6121 (mmt) REVERT: A 262 LYS cc_start: 0.7989 (tmtt) cc_final: 0.7537 (mtmt) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.1557 time to fit residues: 8.0942 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.094799 restraints weight = 5130.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095699 restraints weight = 4285.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096240 restraints weight = 3549.550| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.7893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3366 Z= 0.174 Angle : 0.495 5.438 4562 Z= 0.256 Chirality : 0.045 0.131 497 Planarity : 0.004 0.031 584 Dihedral : 5.212 49.665 463 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 23.46 % Favored : 74.49 % 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: -1.18 (0.41), residues: 417 helix: -0.03 (0.39), residues: 197 sheet: -0.83 (0.68), residues: 60 loop : -1.61 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.004 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.019 0.001 TYR A 225 ARG 0.001 0.000 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.25 seconds wall clock time: 22 minutes 55.78 seconds (1375.78 seconds total)