Starting phenix.real_space_refine on Tue Mar 3 11:31:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jnc_9847/03_2026/6jnc_9847.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jnc_9847/03_2026/6jnc_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2026/6jnc_9847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2026/6jnc_9847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2026/6jnc_9847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jnc_9847/03_2026/6jnc_9847.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.90, per 1000 atoms: 0.27 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: 0.25 Conformation dependent library (CDL) restraints added in 119.7 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: 0.09 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: 0.34 Time building geometry restraints manager: 0.36 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: 0.970 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.260 Find NCS groups from input model: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.500 ------------------------------------------------------------------------------- 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= 0.361 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.001 ARG A 166 TYR 0.012 0.002 TYR A 363 PHE 0.011 0.002 PHE A 57 TRP 0.016 0.002 TRP A 30 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00854 ( 3366) covalent geometry : angle 0.87204 ( 4562) hydrogen bonds : bond 0.31950 ( 118) hydrogen bonds : angle 10.01944 ( 384) *********************** 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 : 0.124 Fit side-chains revert: symmetry clash REVERT: A 5 ASP cc_start: 0.7896 (t70) cc_final: 0.7314 (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: 0.6622 (p) outliers start: 31 outliers final: 5 residues processed: 105 average time/residue: 0.0731 time to fit residues: 9.1081 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 : 0.089 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.0670 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.0470 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.125406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097954 restraints weight = 5074.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099797 restraints weight = 4073.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.099958 restraints weight = 2967.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.101028 restraints weight = 2543.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100940 restraints weight = 2178.229| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3040 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= 0.110 Angle : 0.531 6.353 4562 Z= 0.286 Chirality : 0.045 0.141 497 Planarity : 0.006 0.043 584 Dihedral : 7.261 55.998 474 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.99 % Allowed : 15.54 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.34), residues: 417 helix: -2.90 (0.28), residues: 195 sheet: -1.18 (0.65), residues: 62 loop : -2.51 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.033 0.001 TYR A 225 PHE 0.007 0.001 PHE A 197 TRP 0.011 0.001 TRP A 263 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3366) covalent geometry : angle 0.53067 ( 4562) hydrogen bonds : bond 0.04046 ( 118) hydrogen bonds : angle 4.99141 ( 384) *********************** 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 70 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 5 ASP cc_start: 0.7678 (t70) cc_final: 0.7294 (t0) REVERT: A 69 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7481 (ttmt) REVERT: A 91 THR cc_start: 0.8714 (t) cc_final: 0.8484 (m) REVERT: A 180 SER cc_start: 0.7817 (p) cc_final: 0.7428 (m) REVERT: A 246 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5480 (ttt90) REVERT: A 400 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.5850 (t80) outliers start: 17 outliers final: 7 residues processed: 67 average time/residue: 0.0679 time to fit residues: 5.5808 Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.093306 restraints weight = 5185.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.092276 restraints weight = 4144.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092824 restraints weight = 3917.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.093211 restraints weight = 3353.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.094091 restraints weight = 2961.647| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3366 Z= 0.218 Angle : 0.610 4.731 4562 Z= 0.331 Chirality : 0.049 0.148 497 Planarity : 0.005 0.037 584 Dihedral : 6.876 49.491 471 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.40 % Allowed : 19.06 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.36), residues: 417 helix: -1.96 (0.32), residues: 194 sheet: -1.42 (0.66), residues: 56 loop : -2.26 (0.43), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 265 TYR 0.026 0.002 TYR A 225 PHE 0.014 0.002 PHE A 341 TRP 0.017 0.002 TRP A 89 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 3366) covalent geometry : angle 0.60996 ( 4562) hydrogen bonds : bond 0.05226 ( 118) hydrogen bonds : angle 5.09581 ( 384) *********************** 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: 15 poor density : 47 time to evaluate : 0.123 Fit side-chains REVERT: A 26 GLU cc_start: 0.8487 (pt0) cc_final: 0.7452 (tt0) REVERT: A 246 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6128 (ttt90) REVERT: A 331 ARG cc_start: 0.7772 (ptm160) cc_final: 0.7115 (tmm-80) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 0.0766 time to fit residues: 5.4509 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 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 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.123333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.096284 restraints weight = 5091.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096995 restraints weight = 4174.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097400 restraints weight = 3810.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098034 restraints weight = 3051.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098203 restraints weight = 2620.295| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3366 Z= 0.104 Angle : 0.477 5.054 4562 Z= 0.260 Chirality : 0.045 0.132 497 Planarity : 0.004 0.030 584 Dihedral : 5.377 40.650 465 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.23 % Allowed : 19.35 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.38), residues: 417 helix: -1.25 (0.36), residues: 197 sheet: -1.16 (0.66), residues: 60 loop : -2.15 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.028 0.001 TYR A 225 PHE 0.007 0.001 PHE A 341 TRP 0.008 0.001 TRP A 63 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3366) covalent geometry : angle 0.47711 ( 4562) hydrogen bonds : bond 0.03473 ( 118) hydrogen bonds : angle 4.37845 ( 384) *********************** 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 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.130 Fit side-chains REVERT: A 26 GLU cc_start: 0.8529 (pt0) cc_final: 0.7345 (tt0) REVERT: A 246 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6067 (ttt90) outliers start: 11 outliers final: 5 residues processed: 49 average time/residue: 0.0580 time to fit residues: 3.6049 Evaluate side-chains 41 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 279 ILE 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 29 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.120566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.093624 restraints weight = 5119.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094323 restraints weight = 4401.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094940 restraints weight = 3746.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095333 restraints weight = 3136.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095538 restraints weight = 2799.714| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3366 Z= 0.130 Angle : 0.492 4.406 4562 Z= 0.263 Chirality : 0.046 0.135 497 Planarity : 0.004 0.031 584 Dihedral : 5.368 37.063 465 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.39), residues: 417 helix: -0.85 (0.37), residues: 197 sheet: -1.06 (0.68), residues: 60 loop : -1.99 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 265 TYR 0.023 0.001 TYR A 225 PHE 0.009 0.001 PHE A 341 TRP 0.009 0.001 TRP A 30 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3366) covalent geometry : angle 0.49240 ( 4562) hydrogen bonds : bond 0.03710 ( 118) hydrogen bonds : angle 4.37819 ( 384) *********************** 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: 11 poor density : 36 time to evaluate : 0.129 Fit side-chains REVERT: A 237 MET cc_start: 0.5258 (ttm) cc_final: 0.4871 (ttm) outliers start: 11 outliers final: 10 residues processed: 43 average time/residue: 0.0535 time to fit residues: 3.0597 Evaluate side-chains 44 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR 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 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 27 optimal weight: 20.0000 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.120635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.093657 restraints weight = 5116.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094818 restraints weight = 4412.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.094965 restraints weight = 4147.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095370 restraints weight = 3265.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.095859 restraints weight = 2769.605| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.7260 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= 0.117 Angle : 0.464 4.255 4562 Z= 0.248 Chirality : 0.045 0.130 497 Planarity : 0.004 0.030 584 Dihedral : 4.762 36.547 461 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.40), residues: 417 helix: -0.52 (0.38), residues: 197 sheet: -0.86 (0.69), residues: 60 loop : -1.87 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.017 0.001 TYR A 225 PHE 0.007 0.001 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3366) covalent geometry : angle 0.46441 ( 4562) hydrogen bonds : bond 0.03377 ( 118) hydrogen bonds : angle 4.21893 ( 384) *********************** 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 : 0.128 Fit side-chains REVERT: A 26 GLU cc_start: 0.8593 (pt0) cc_final: 0.7651 (tt0) REVERT: A 218 GLN cc_start: 0.8384 (tt0) cc_final: 0.7905 (tp40) REVERT: A 262 LYS cc_start: 0.8121 (tmtt) cc_final: 0.7630 (mtmt) REVERT: A 408 TYR cc_start: 0.8565 (t80) cc_final: 0.8304 (t80) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.0534 time to fit residues: 3.1016 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 : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 269 SER 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 12 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.121598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094434 restraints weight = 5181.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095570 restraints weight = 4481.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095681 restraints weight = 4273.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.096115 restraints weight = 3336.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.096327 restraints weight = 2822.602| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.7428 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= 0.108 Angle : 0.453 4.154 4562 Z= 0.240 Chirality : 0.045 0.130 497 Planarity : 0.004 0.030 584 Dihedral : 4.589 36.339 459 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 19.65 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.41), residues: 417 helix: -0.35 (0.39), residues: 198 sheet: -0.81 (0.68), residues: 60 loop : -1.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.018 0.001 TYR A 225 PHE 0.007 0.001 PHE A 341 TRP 0.007 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 3366) covalent geometry : angle 0.45263 ( 4562) hydrogen bonds : bond 0.03365 ( 118) hydrogen bonds : angle 4.13988 ( 384) *********************** 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 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.148 Fit side-chains REVERT: A 218 GLN cc_start: 0.8442 (tt0) cc_final: 0.8047 (tp40) REVERT: A 237 MET cc_start: 0.5222 (ttm) cc_final: 0.4702 (ttm) REVERT: A 262 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7637 (mtmt) REVERT: A 265 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7381 (mmm-85) REVERT: A 408 TYR cc_start: 0.8529 (t80) cc_final: 0.8280 (t80) outliers start: 12 outliers final: 11 residues processed: 45 average time/residue: 0.0552 time to fit residues: 3.2879 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER 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 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.118632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.091748 restraints weight = 5225.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.092378 restraints weight = 4645.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.093001 restraints weight = 4009.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.093401 restraints weight = 3252.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.093693 restraints weight = 2846.927| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.7589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3366 Z= 0.165 Angle : 0.502 5.204 4562 Z= 0.266 Chirality : 0.047 0.168 497 Planarity : 0.004 0.031 584 Dihedral : 4.987 38.945 459 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.81 % Allowed : 19.06 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.41), residues: 417 helix: -0.31 (0.39), residues: 198 sheet: -0.70 (0.69), residues: 60 loop : -1.82 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.019 0.001 TYR A 225 PHE 0.010 0.001 PHE A 341 TRP 0.009 0.001 TRP A 30 HIS 0.005 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3366) covalent geometry : angle 0.50248 ( 4562) hydrogen bonds : bond 0.04023 ( 118) hydrogen bonds : angle 4.39422 ( 384) *********************** 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: 13 poor density : 35 time to evaluate : 0.110 Fit side-chains REVERT: A 218 GLN cc_start: 0.8480 (tt0) cc_final: 0.8205 (tp40) REVERT: A 262 LYS cc_start: 0.8198 (tmtt) cc_final: 0.7709 (mtmt) REVERT: A 265 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7390 (mmm-85) REVERT: A 278 ASN cc_start: 0.6853 (t0) cc_final: 0.6592 (t0) outliers start: 13 outliers final: 12 residues processed: 45 average time/residue: 0.0389 time to fit residues: 2.3876 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER 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 377 MET 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 0 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 0.0570 chunk 31 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.119601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.092172 restraints weight = 5194.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.092633 restraints weight = 3745.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.092933 restraints weight = 3477.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.093429 restraints weight = 2994.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.094075 restraints weight = 2620.016| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.7735 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= 0.113 Angle : 0.461 5.096 4562 Z= 0.244 Chirality : 0.045 0.132 497 Planarity : 0.004 0.030 584 Dihedral : 4.801 42.311 459 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.52 % Allowed : 20.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.41), residues: 417 helix: -0.11 (0.39), residues: 198 sheet: -0.59 (0.70), residues: 60 loop : -1.72 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 331 TYR 0.019 0.001 TYR A 225 PHE 0.006 0.001 PHE A 341 TRP 0.007 0.001 TRP A 92 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3366) covalent geometry : angle 0.46092 ( 4562) hydrogen bonds : bond 0.03388 ( 118) hydrogen bonds : angle 4.17870 ( 384) *********************** 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.122 Fit side-chains REVERT: A 218 GLN cc_start: 0.8462 (tt0) cc_final: 0.8160 (tp40) REVERT: A 262 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7690 (mtmt) REVERT: A 265 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7384 (mmm-85) REVERT: A 278 ASN cc_start: 0.6848 (t0) cc_final: 0.6578 (t0) outliers start: 12 outliers final: 12 residues processed: 44 average time/residue: 0.0476 time to fit residues: 2.8239 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER 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 377 MET Chi-restraints excluded: chain A residue 393 ILE 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 11 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 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 = 0.3341 r_free = 0.3341 target = 0.117704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.090831 restraints weight = 5236.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.091328 restraints weight = 4634.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.091770 restraints weight = 4229.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.092243 restraints weight = 3393.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.092640 restraints weight = 2990.668| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3366 Z= 0.191 Angle : 0.526 4.878 4562 Z= 0.277 Chirality : 0.047 0.144 497 Planarity : 0.004 0.029 584 Dihedral : 5.374 55.163 459 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.52 % Allowed : 20.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.41), residues: 417 helix: -0.21 (0.39), residues: 198 sheet: -0.70 (0.68), residues: 60 loop : -1.83 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 166 TYR 0.018 0.001 TYR A 225 PHE 0.010 0.001 PHE A 341 TRP 0.010 0.001 TRP A 89 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 3366) covalent geometry : angle 0.52623 ( 4562) hydrogen bonds : bond 0.04196 ( 118) hydrogen bonds : angle 4.48983 ( 384) ********************** 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.133 Fit side-chains REVERT: A 218 GLN cc_start: 0.8463 (tt0) cc_final: 0.8226 (tp40) REVERT: A 262 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7754 (mtmt) outliers start: 12 outliers final: 11 residues processed: 44 average time/residue: 0.0515 time to fit residues: 3.0344 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 184 SER 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 Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.121271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.094203 restraints weight = 5256.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.095693 restraints weight = 4517.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.095689 restraints weight = 4152.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.096057 restraints weight = 3335.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.096536 restraints weight = 2796.373| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.7880 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= 0.100 Angle : 0.456 5.273 4562 Z= 0.243 Chirality : 0.045 0.173 497 Planarity : 0.004 0.030 584 Dihedral : 4.951 52.808 459 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.41), residues: 417 helix: 0.05 (0.40), residues: 198 sheet: -0.47 (0.71), residues: 60 loop : -1.73 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.036 0.001 TYR A 225 PHE 0.005 0.001 PHE A 341 TRP 0.008 0.001 TRP A 92 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3366) covalent geometry : angle 0.45602 ( 4562) hydrogen bonds : bond 0.03295 ( 118) hydrogen bonds : angle 4.18570 ( 384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 654.13 seconds wall clock time: 11 minutes 51.76 seconds (711.76 seconds total)