Starting phenix.real_space_refine on Mon Feb 10 23:46:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jnc_9847/02_2025/6jnc_9847.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnc_9847/02_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_9847/02_2025/6jnc_9847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnc_9847/02_2025/6jnc_9847.map" model { file = "/net/cci-nas-00/data/ceres_data/6jnc_9847/02_2025/6jnc_9847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnc_9847/02_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-5592/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: 2.77, per 1000 atoms: 0.84 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: 0.82 Conformation dependent library (CDL) restraints added in 435.6 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: 0.40 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: 0.87 Time building geometry restraints manager: 0.96 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: 0.540 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.030 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- 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 : 0.397 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: 0.1854 time to fit residues: 22.9767 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 : 0.341 ------------------------------------------------------------------------------- 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: 8.9990 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 = 0.097388 restraints weight = 5020.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098004 restraints weight = 3784.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.098716 restraints weight = 3477.326| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 : 0.349 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7376 (ttmt) REVERT: A 91 THR cc_start: 0.8674 (t) cc_final: 0.8380 (m) REVERT: A 180 SER cc_start: 0.7853 (p) cc_final: 0.7416 (m) REVERT: A 246 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5492 (ttt90) REVERT: A 331 ARG cc_start: 0.7393 (tmm-80) cc_final: 0.6981 (ptm-80) REVERT: A 400 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.5858 (t80) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 0.1634 time to fit residues: 14.1367 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 : 0.339 ------------------------------------------------------------------------------- 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: 0.0020 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.7794 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.124588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097334 restraints weight = 5011.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.097266 restraints weight = 3986.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097820 restraints weight = 3811.172| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5029 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= 0.211 Angle : 0.524 4.797 4562 Z= 0.284 Chirality : 0.047 0.168 497 Planarity : 0.005 0.035 584 Dihedral : 6.354 45.562 471 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.81 % Allowed : 19.94 % Favored : 76.25 % 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: -2.89 (0.37), residues: 417 helix: -1.78 (0.34), residues: 195 sheet: -1.51 (0.63), residues: 60 loop : -2.03 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 63 HIS 0.002 0.001 HIS A 267 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 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 61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.390 Fit side-chains REVERT: A 26 GLU cc_start: 0.8269 (pt0) cc_final: 0.7025 (tt0) REVERT: A 69 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8101 (ttmt) REVERT: A 145 ASP cc_start: 0.7645 (t0) cc_final: 0.7431 (t0) REVERT: A 180 SER cc_start: 0.8541 (p) cc_final: 0.8182 (m) REVERT: A 246 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.5598 (ttt90) REVERT: A 408 TYR cc_start: 0.8652 (t80) cc_final: 0.8241 (t80) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.1591 time to fit residues: 11.6115 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** A 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090272 restraints weight = 5304.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091456 restraints weight = 4269.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.092261 restraints weight = 3841.530| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3366 Z= 0.422 Angle : 0.637 7.909 4562 Z= 0.338 Chirality : 0.051 0.150 497 Planarity : 0.005 0.036 584 Dihedral : 6.968 50.033 471 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.40 % Allowed : 20.53 % Favored : 75.07 % 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: -2.80 (0.38), residues: 417 helix: -1.63 (0.35), residues: 196 sheet: -1.17 (0.73), residues: 54 loop : -2.22 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 30 HIS 0.006 0.002 HIS A 388 PHE 0.014 0.002 PHE A 341 TYR 0.024 0.002 TYR A 225 ARG 0.003 0.001 ARG A 331 *********************** 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 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.382 Fit side-chains REVERT: A 26 GLU cc_start: 0.8693 (pt0) cc_final: 0.7696 (tt0) REVERT: A 69 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8339 (ttmt) REVERT: A 246 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6220 (ttt90) REVERT: A 377 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9011 (mmm) REVERT: A 408 TYR cc_start: 0.8724 (t80) cc_final: 0.8462 (t80) outliers start: 15 outliers final: 6 residues processed: 47 average time/residue: 0.1784 time to fit residues: 10.3088 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 : 0.388 ------------------------------------------------------------------------------- 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 377 MET 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: 4.9990 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 358 ASN A 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093794 restraints weight = 5148.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094516 restraints weight = 4118.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.095034 restraints weight = 3825.057| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3366 Z= 0.149 Angle : 0.471 4.407 4562 Z= 0.254 Chirality : 0.045 0.133 497 Planarity : 0.004 0.032 584 Dihedral : 6.051 49.658 469 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.93 % Allowed : 21.11 % Favored : 75.95 % 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: -2.27 (0.39), residues: 417 helix: -1.10 (0.36), residues: 196 sheet: -1.13 (0.69), residues: 60 loop : -2.01 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 92 HIS 0.002 0.001 HIS A 388 PHE 0.005 0.001 PHE A 341 TYR 0.024 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.392 Fit side-chains REVERT: A 69 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8255 (ttmt) REVERT: A 218 GLN cc_start: 0.8330 (tt0) cc_final: 0.8041 (tp40) REVERT: A 246 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6094 (ttt90) REVERT: A 287 LEU cc_start: 0.8262 (mt) cc_final: 0.8025 (mp) outliers start: 10 outliers final: 6 residues processed: 44 average time/residue: 0.1743 time to fit residues: 9.4882 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 : 0.367 ------------------------------------------------------------------------------- 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 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 377 MET 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: 1.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.090807 restraints weight = 5339.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.091666 restraints weight = 4301.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.092510 restraints weight = 4023.415| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3366 Z= 0.311 Angle : 0.549 5.054 4562 Z= 0.290 Chirality : 0.048 0.143 497 Planarity : 0.004 0.034 584 Dihedral : 6.532 50.383 469 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.52 % Allowed : 21.41 % Favored : 75.07 % 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: -2.13 (0.39), residues: 417 helix: -0.88 (0.37), residues: 192 sheet: -1.20 (0.70), residues: 58 loop : -2.00 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.022 0.001 TYR A 225 ARG 0.003 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 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.387 Fit side-chains REVERT: A 26 GLU cc_start: 0.8649 (pt0) cc_final: 0.7737 (tt0) REVERT: A 69 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8345 (ttmt) REVERT: A 218 GLN cc_start: 0.8482 (tt0) cc_final: 0.8212 (tp40) outliers start: 12 outliers final: 7 residues processed: 42 average time/residue: 0.1634 time to fit residues: 8.6242 Evaluate side-chains 42 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 284 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 377 MET 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: 6.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3340 r_free = 0.3340 target = 0.117992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.092038 restraints weight = 5142.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092709 restraints weight = 4140.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.093580 restraints weight = 4021.086| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3366 Z= 0.246 Angle : 0.504 4.811 4562 Z= 0.268 Chirality : 0.047 0.169 497 Planarity : 0.004 0.034 584 Dihedral : 5.980 53.766 463 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: -1.98 (0.40), residues: 417 helix: -0.78 (0.37), residues: 197 sheet: -1.12 (0.69), residues: 60 loop : -1.91 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.028 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.363 Fit side-chains REVERT: A 69 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8311 (ttmt) REVERT: A 218 GLN cc_start: 0.8501 (tt0) cc_final: 0.8235 (tp40) REVERT: A 249 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7672 (pt) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.1612 time to fit residues: 8.9413 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.120674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.094745 restraints weight = 5099.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095228 restraints weight = 4183.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095360 restraints weight = 4201.446| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3366 Z= 0.143 Angle : 0.463 6.731 4562 Z= 0.244 Chirality : 0.045 0.203 497 Planarity : 0.004 0.030 584 Dihedral : 5.281 49.833 463 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 22.87 % 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: -1.59 (0.40), residues: 417 helix: -0.48 (0.38), residues: 197 sheet: -0.86 (0.70), residues: 60 loop : -1.72 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.003 0.001 HIS A 388 PHE 0.005 0.001 PHE A 57 TYR 0.019 0.001 TYR A 225 ARG 0.001 0.000 ARG A 396 *********************** 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.411 Fit side-chains REVERT: A 69 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8125 (ttmt) REVERT: A 218 GLN cc_start: 0.8402 (tt0) cc_final: 0.8184 (tp40) REVERT: A 262 LYS cc_start: 0.8008 (tmtt) cc_final: 0.7578 (mtmt) REVERT: A 279 ILE cc_start: 0.7757 (mm) cc_final: 0.7319 (pt) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.1627 time to fit residues: 9.0281 Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 27 optimal weight: 0.0270 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.8042 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.120368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094299 restraints weight = 5151.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094600 restraints weight = 4317.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094821 restraints weight = 4308.339| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3366 Z= 0.187 Angle : 0.485 4.849 4562 Z= 0.255 Chirality : 0.046 0.210 497 Planarity : 0.004 0.030 584 Dihedral : 5.271 48.965 463 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.35 % Allowed : 23.75 % 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: -1.48 (0.41), residues: 417 helix: -0.36 (0.38), residues: 197 sheet: -0.84 (0.69), residues: 60 loop : -1.70 (0.45), 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 0.007 0.001 PHE A 341 TYR 0.034 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: 8 poor density : 36 time to evaluate : 0.398 Fit side-chains REVERT: A 69 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8177 (ttmt) REVERT: A 262 LYS cc_start: 0.8047 (tmtt) cc_final: 0.7637 (mtmt) REVERT: A 279 ILE cc_start: 0.7794 (mm) cc_final: 0.7536 (pt) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.1533 time to fit residues: 8.3401 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 : 0.382 ------------------------------------------------------------------------------- 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 269 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.3980 chunk 6 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.123839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098265 restraints weight = 5007.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.098347 restraints weight = 4868.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098582 restraints weight = 4043.415| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.7894 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= 0.124 Angle : 0.467 5.353 4562 Z= 0.247 Chirality : 0.045 0.187 497 Planarity : 0.004 0.030 584 Dihedral : 5.014 48.727 463 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.76 % Allowed : 24.05 % Favored : 74.19 % 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: -1.04 (0.41), residues: 417 helix: -0.03 (0.39), residues: 197 sheet: -0.46 (0.72), residues: 60 loop : -1.51 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.003 0.001 HIS A 388 PHE 0.005 0.001 PHE A 57 TYR 0.036 0.001 TYR A 225 ARG 0.002 0.000 ARG A 246 ********************** 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 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.411 Fit side-chains REVERT: A 262 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7591 (mtmt) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.1695 time to fit residues: 9.4237 Evaluate side-chains 40 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 269 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 13 optimal weight: 0.0040 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 overall best weight: 1.0014 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.122987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097546 restraints weight = 5108.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098141 restraints weight = 4328.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098915 restraints weight = 3621.661| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.7944 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= 0.142 Angle : 0.468 5.320 4562 Z= 0.244 Chirality : 0.045 0.157 497 Planarity : 0.004 0.031 584 Dihedral : 4.302 32.901 459 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.05 % Allowed : 24.34 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.41), residues: 417 helix: 0.10 (0.39), residues: 195 sheet: -0.33 (0.73), residues: 60 loop : -1.45 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 382 HIS 0.003 0.001 HIS A 388 PHE 0.005 0.001 PHE A 341 TYR 0.016 0.001 TYR A 225 ARG 0.001 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1236.53 seconds wall clock time: 22 minutes 55.99 seconds (1375.99 seconds total)