Starting phenix.real_space_refine on Thu Mar 6 03:55:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lto_23517/03_2025/7lto_23517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lto_23517/03_2025/7lto_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2025/7lto_23517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2025/7lto_23517.map" model { file = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2025/7lto_23517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2025/7lto_23517.cif" } resolution = 3.2 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= -0.000 sd= 0.003 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 26 5.16 5 C 3114 2.51 5 N 776 2.21 5 O 838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2876 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain breaks: 4 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.33, per 1000 atoms: 0.70 Number of scatterers: 4754 At special positions: 0 Unit cell: (64.904, 77.672, 101.08, 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 26 16.00 O 838 8.00 N 776 7.00 C 3114 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: 1.07 Conformation dependent library (CDL) restraints added in 525.4 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.985A pdb=" N GLN A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.714A pdb=" N PHE A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.329A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.550A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.569A pdb=" N ASP A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 609 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: 1.00 Time building geometry restraints manager: 1.29 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: 1470 1.34 - 1.46: 861 1.46 - 1.58: 2484 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4853 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.228 0.016 1.00e-02 1.00e+04 2.43e+00 bond pdb=" C TRP A 240 " pdb=" O TRP A 240 " ideal model delta sigma weight residual 1.236 1.219 0.018 1.29e-02 6.01e+03 1.85e+00 ... (remaining 4848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 6247 1.45 - 2.89: 247 2.89 - 4.34: 49 4.34 - 5.78: 13 5.78 - 7.23: 7 Bond angle restraints: 6563 Sorted by residual: angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N TRP A 240 " pdb=" CA TRP A 240 " pdb=" C TRP A 240 " ideal model delta sigma weight residual 112.23 119.19 -6.96 1.26e+00 6.30e-01 3.06e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 114.09 106.86 7.23 1.55e+00 4.16e-01 2.17e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 112.04 105.82 6.22 1.44e+00 4.82e-01 1.86e+01 ... (remaining 6558 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2596 17.82 - 35.64: 241 35.64 - 53.46: 58 53.46 - 71.28: 10 71.28 - 89.11: 5 Dihedral angle restraints: 2910 sinusoidal: 1106 harmonic: 1804 Sorted by residual: dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA SER A 411 " pdb=" C SER A 411 " pdb=" N TYR A 412 " pdb=" CA TYR A 412 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASN B 345 " pdb=" C ASN B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 695 0.075 - 0.150: 54 0.150 - 0.225: 7 0.225 - 0.299: 3 0.299 - 0.374: 1 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA TYR A 81 " pdb=" N TYR A 81 " pdb=" C TYR A 81 " pdb=" CB TYR A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR A 82 " pdb=" N TYR A 82 " pdb=" C TYR A 82 " pdb=" CB TYR A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 757 not shown) Planarity restraints: 819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 239 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C ILE A 239 " 0.028 2.00e-02 2.50e+03 pdb=" O ILE A 239 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 240 " -0.009 2.00e-02 2.50e+03 ... (remaining 816 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 929 2.77 - 3.30: 4572 3.30 - 3.83: 7256 3.83 - 4.37: 9095 4.37 - 4.90: 15381 Nonbonded interactions: 37233 Sorted by model distance: nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 3.120 nonbonded pdb=" O ARG A 387 " pdb=" OG SER A 391 " model vdw 2.281 3.040 nonbonded pdb=" O LYS A 343 " pdb=" OG SER A 347 " model vdw 2.282 3.040 nonbonded pdb=" NZ LYS A 207 " pdb=" O VAL A 321 " model vdw 2.311 3.120 nonbonded pdb=" NE2 GLN B 370 " pdb=" O THR B 414 " model vdw 2.311 3.120 ... (remaining 37228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.003 0.032 4853 Z= 0.219 Angle : 0.707 7.229 6563 Z= 0.447 Chirality : 0.049 0.374 760 Planarity : 0.003 0.037 819 Dihedral : 15.408 89.105 1726 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.29), residues: 583 helix: -2.13 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -3.81 (0.31), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.002 0.000 HIS A 46 PHE 0.011 0.001 PHE A 413 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 337 LYS cc_start: 0.8674 (mttm) cc_final: 0.8441 (mmmt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.1807 time to fit residues: 25.1794 Evaluate side-chains 88 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 345 GLN A 383 GLN B 201 HIS B 206 ASN B 211 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 GLN B 407 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.176428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158831 restraints weight = 6137.430| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.55 r_work: 0.3872 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4853 Z= 0.176 Angle : 0.565 6.907 6563 Z= 0.289 Chirality : 0.040 0.145 760 Planarity : 0.004 0.039 819 Dihedral : 6.402 51.118 660 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.05 % Allowed : 16.87 % Favored : 80.08 % 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: -2.67 (0.32), residues: 583 helix: -0.71 (0.28), residues: 343 sheet: None (None), residues: 0 loop : -3.42 (0.32), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 240 HIS 0.003 0.001 HIS A 46 PHE 0.012 0.001 PHE B 348 TYR 0.021 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.554 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.1457 time to fit residues: 19.3616 Evaluate side-chains 98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 41 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 339 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.176844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160644 restraints weight = 6166.382| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.40 r_work: 0.3881 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4853 Z= 0.176 Angle : 0.544 6.980 6563 Z= 0.274 Chirality : 0.039 0.129 760 Planarity : 0.003 0.042 819 Dihedral : 6.093 49.401 656 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.46 % Allowed : 18.29 % Favored : 78.25 % 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: -1.78 (0.34), residues: 583 helix: 0.01 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -3.11 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 240 HIS 0.001 0.000 HIS A 261 PHE 0.013 0.001 PHE B 396 TYR 0.009 0.001 TYR B 209 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.566 Fit side-chains REVERT: B 369 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8464 (pp) REVERT: B 450 ILE cc_start: 0.7220 (mp) cc_final: 0.6715 (mp) outliers start: 17 outliers final: 10 residues processed: 106 average time/residue: 0.1400 time to fit residues: 19.9061 Evaluate side-chains 99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 508 GLN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.176825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160699 restraints weight = 6220.448| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.40 r_work: 0.3881 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.176 Angle : 0.552 7.081 6563 Z= 0.275 Chirality : 0.039 0.125 760 Planarity : 0.003 0.044 819 Dihedral : 5.214 48.026 648 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.25 % Allowed : 19.92 % 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 (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: -1.36 (0.35), residues: 583 helix: 0.38 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -2.93 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.012 0.001 PHE B 348 TYR 0.020 0.001 TYR B 432 ARG 0.001 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: B 339 ASN cc_start: 0.7772 (t0) cc_final: 0.5958 (m110) REVERT: B 369 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8456 (pp) REVERT: B 450 ILE cc_start: 0.7310 (mp) cc_final: 0.6778 (mp) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.1359 time to fit residues: 18.0292 Evaluate side-chains 94 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.173487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156428 restraints weight = 6289.324| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.55 r_work: 0.3825 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4853 Z= 0.254 Angle : 0.610 10.589 6563 Z= 0.303 Chirality : 0.041 0.124 760 Planarity : 0.003 0.046 819 Dihedral : 5.380 51.829 647 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.27 % Allowed : 18.50 % Favored : 77.24 % 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: -1.37 (0.34), residues: 583 helix: 0.30 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -2.82 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 200 HIS 0.002 0.001 HIS B 342 PHE 0.017 0.002 PHE B 348 TYR 0.015 0.001 TYR B 209 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: B 336 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: B 369 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8487 (pp) REVERT: B 450 ILE cc_start: 0.7278 (mp) cc_final: 0.6729 (mp) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.1376 time to fit residues: 18.9822 Evaluate side-chains 98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.0070 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN B 354 ASN B 389 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.174000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156230 restraints weight = 6257.819| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.66 r_work: 0.3832 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.219 Angle : 0.619 16.472 6563 Z= 0.302 Chirality : 0.041 0.122 760 Planarity : 0.003 0.046 819 Dihedral : 5.334 53.168 647 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.27 % Allowed : 21.14 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.34), residues: 583 helix: 0.43 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -2.72 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.015 0.002 PHE B 348 TYR 0.014 0.001 TYR B 209 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: B 369 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8463 (pp) REVERT: B 450 ILE cc_start: 0.7371 (mp) cc_final: 0.6822 (mp) outliers start: 21 outliers final: 14 residues processed: 99 average time/residue: 0.1429 time to fit residues: 18.8199 Evaluate side-chains 95 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.174090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157162 restraints weight = 6112.671| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.54 r_work: 0.3836 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4853 Z= 0.227 Angle : 0.618 14.842 6563 Z= 0.303 Chirality : 0.041 0.121 760 Planarity : 0.003 0.047 819 Dihedral : 5.384 55.728 647 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.47 % Allowed : 21.75 % Favored : 73.78 % 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: -1.13 (0.35), residues: 583 helix: 0.48 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -2.68 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.002 0.000 HIS B 342 PHE 0.015 0.002 PHE B 348 TYR 0.020 0.001 TYR B 432 ARG 0.003 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: B 369 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 450 ILE cc_start: 0.7320 (mp) cc_final: 0.6785 (mp) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.1397 time to fit residues: 17.9093 Evaluate side-chains 95 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 20 optimal weight: 0.0570 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN B 277 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.175231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158294 restraints weight = 6156.253| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.56 r_work: 0.3854 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4853 Z= 0.201 Angle : 0.607 14.225 6563 Z= 0.299 Chirality : 0.040 0.122 760 Planarity : 0.003 0.047 819 Dihedral : 5.324 55.709 647 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.27 % Allowed : 21.95 % Favored : 73.78 % 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: -0.98 (0.35), residues: 583 helix: 0.61 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -2.64 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.014 0.001 PHE B 348 TYR 0.013 0.001 TYR B 209 ARG 0.004 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: A 424 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 369 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8452 (pp) REVERT: B 450 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6799 (mp) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.1441 time to fit residues: 17.7800 Evaluate side-chains 95 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN B 342 HIS B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.177465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.158505 restraints weight = 6287.250| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.71 r_work: 0.3876 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4853 Z= 0.160 Angle : 0.573 13.224 6563 Z= 0.282 Chirality : 0.039 0.121 760 Planarity : 0.003 0.047 819 Dihedral : 5.039 54.065 647 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.66 % Allowed : 22.56 % Favored : 73.78 % 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: -0.69 (0.35), residues: 583 helix: 0.84 (0.30), residues: 348 sheet: None (None), residues: 0 loop : -2.57 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 200 HIS 0.001 0.000 HIS B 342 PHE 0.010 0.001 PHE A 55 TYR 0.017 0.001 TYR B 432 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8731 (p) cc_final: 0.8369 (p) REVERT: A 257 TYR cc_start: 0.6958 (t80) cc_final: 0.6755 (t80) REVERT: A 387 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7862 (ttm-80) REVERT: B 292 MET cc_start: 0.7926 (ttp) cc_final: 0.7675 (ttt) REVERT: B 369 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8418 (pp) REVERT: B 450 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6808 (mp) outliers start: 18 outliers final: 14 residues processed: 97 average time/residue: 0.1363 time to fit residues: 17.6199 Evaluate side-chains 99 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 47 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.0070 chunk 56 optimal weight: 0.0370 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.178335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160971 restraints weight = 6143.635| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.50 r_work: 0.3893 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4853 Z= 0.166 Angle : 0.591 12.899 6563 Z= 0.290 Chirality : 0.039 0.121 760 Planarity : 0.003 0.047 819 Dihedral : 4.960 54.330 647 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.05 % Allowed : 23.58 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.36), residues: 583 helix: 0.96 (0.30), residues: 348 sheet: None (None), residues: 0 loop : -2.56 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 PHE 0.018 0.001 PHE A 285 TYR 0.008 0.001 TYR B 209 ARG 0.001 0.000 ARG A 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8661 (p) cc_final: 0.8304 (p) REVERT: A 387 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7702 (ttm-80) REVERT: B 292 MET cc_start: 0.7935 (ttp) cc_final: 0.7710 (ttt) REVERT: B 369 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8430 (pp) REVERT: B 450 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6717 (mp) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.1379 time to fit residues: 17.8667 Evaluate side-chains 100 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159331 restraints weight = 6211.922| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.54 r_work: 0.3876 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4853 Z= 0.193 Angle : 0.608 13.056 6563 Z= 0.297 Chirality : 0.040 0.125 760 Planarity : 0.003 0.047 819 Dihedral : 4.686 55.320 645 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.46 % Allowed : 23.58 % Favored : 72.97 % 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: -0.54 (0.36), residues: 583 helix: 1.00 (0.30), residues: 346 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 368 PHE 0.019 0.001 PHE A 285 TYR 0.020 0.001 TYR B 432 ARG 0.001 0.000 ARG A 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.71 seconds wall clock time: 51 minutes 40.94 seconds (3100.94 seconds total)