Starting phenix.real_space_refine on Tue Mar 3 13:03:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lto_23517/03_2026/7lto_23517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lto_23517/03_2026/7lto_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_2026/7lto_23517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2026/7lto_23517.map" model { file = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2026/7lto_23517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lto_23517/03_2026/7lto_23517.cif" } resolution = 3.2 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= -0.000 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): 0.00s 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: 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: {'ASP:plan': 6, 'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 3, 'TYR:plan': 1, 'HIS:plan': 1} 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: {'TYR:plan': 3, 'ASP:plan': 13, 'GLU:plan': 5, 'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 1.17, per 1000 atoms: 0.25 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: 0.36 Conformation dependent library (CDL) restraints added in 317.9 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: 0.13 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: 0.64 Time building geometry restraints manager: 0.51 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: 1.860 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.700 Find NCS groups from input model: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- 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= 0.193 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 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: -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 ARG 0.001 0.000 ARG A 387 TYR 0.009 0.001 TYR A 82 PHE 0.011 0.001 PHE A 413 TRP 0.012 0.002 TRP B 200 HIS 0.002 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4853) covalent geometry : angle 0.70741 ( 6563) hydrogen bonds : bond 0.21473 ( 203) hydrogen bonds : angle 8.45438 ( 609) *********************** 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 : 0.121 Fit side-chains revert: symmetry clash REVERT: A 337 LYS cc_start: 0.8674 (mttm) cc_final: 0.8440 (mmmt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.0744 time to fit residues: 10.4013 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 : 0.176 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.175479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157917 restraints weight = 6231.893| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.54 r_work: 0.3858 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1637 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= 0.130 Angle : 0.575 6.938 6563 Z= 0.294 Chirality : 0.040 0.145 760 Planarity : 0.004 0.040 819 Dihedral : 6.492 51.465 660 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.05 % Allowed : 17.48 % 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: -2.73 (0.32), residues: 583 helix: -0.77 (0.27), residues: 347 sheet: None (None), residues: 0 loop : -3.47 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.021 0.001 TYR B 432 PHE 0.013 0.001 PHE B 348 TRP 0.013 0.003 TRP A 240 HIS 0.003 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4853) covalent geometry : angle 0.57460 ( 6563) hydrogen bonds : bond 0.04221 ( 203) hydrogen bonds : angle 4.76676 ( 609) *********************** 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 103 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.120 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 98 average time/residue: 0.0571 time to fit residues: 7.5331 Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 339 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 = 0.4155 r_free = 0.4155 target = 0.174312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157914 restraints weight = 6207.870| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.42 r_work: 0.3845 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1859 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= 0.142 Angle : 0.571 7.045 6563 Z= 0.287 Chirality : 0.040 0.131 760 Planarity : 0.003 0.044 819 Dihedral : 6.311 50.603 656 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.07 % Allowed : 17.89 % Favored : 78.05 % 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: -1.93 (0.34), residues: 583 helix: -0.12 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -3.17 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.009 0.001 TYR A 82 PHE 0.015 0.002 PHE B 396 TRP 0.012 0.002 TRP A 240 HIS 0.001 0.000 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4853) covalent geometry : angle 0.57094 ( 6563) hydrogen bonds : bond 0.04023 ( 203) hydrogen bonds : angle 4.40651 ( 609) *********************** 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 109 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.192 Fit side-chains REVERT: B 369 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8524 (pp) outliers start: 20 outliers final: 11 residues processed: 101 average time/residue: 0.0610 time to fit residues: 8.3235 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 : 0.192 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.175510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.159272 restraints weight = 6175.875| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.40 r_work: 0.3859 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2055 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= 0.128 Angle : 0.560 7.027 6563 Z= 0.282 Chirality : 0.040 0.126 760 Planarity : 0.003 0.044 819 Dihedral : 5.788 50.408 650 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.66 % Allowed : 19.72 % Favored : 76.63 % 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: -1.51 (0.34), residues: 583 helix: 0.23 (0.29), residues: 343 sheet: None (None), residues: 0 loop : -2.95 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.019 0.001 TYR B 432 PHE 0.012 0.001 PHE B 343 TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4853) covalent geometry : angle 0.55988 ( 6563) hydrogen bonds : bond 0.03657 ( 203) hydrogen bonds : angle 4.13840 ( 609) *********************** 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 106 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: B 369 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B 450 ILE cc_start: 0.7230 (mp) cc_final: 0.6719 (mp) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.0542 time to fit residues: 7.2344 Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.4172 r_free = 0.4172 target = 0.175724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.158921 restraints weight = 6223.415| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.55 r_work: 0.3852 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4853 Z= 0.131 Angle : 0.583 10.685 6563 Z= 0.288 Chirality : 0.040 0.122 760 Planarity : 0.003 0.044 819 Dihedral : 5.805 50.833 650 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.07 % Allowed : 20.12 % Favored : 75.81 % 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: -1.32 (0.34), residues: 583 helix: 0.37 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -2.84 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 318 TYR 0.015 0.001 TYR B 209 PHE 0.014 0.001 PHE B 343 TRP 0.012 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 4853) covalent geometry : angle 0.58281 ( 6563) hydrogen bonds : bond 0.03622 ( 203) hydrogen bonds : angle 4.09302 ( 609) *********************** 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 105 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8649 (p) cc_final: 0.8320 (p) REVERT: B 369 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8500 (pp) REVERT: B 450 ILE cc_start: 0.7331 (mp) cc_final: 0.6786 (mp) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.0597 time to fit residues: 7.8509 Evaluate side-chains 98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 318 VAL Chi-restraints excluded: chain A residue 361 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 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 = 0.4132 r_free = 0.4132 target = 0.171870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153986 restraints weight = 6326.858| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 1.67 r_work: 0.3805 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4853 Z= 0.177 Angle : 0.649 15.880 6563 Z= 0.317 Chirality : 0.042 0.122 760 Planarity : 0.004 0.045 819 Dihedral : 6.114 54.553 650 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.27 % Allowed : 21.34 % Favored : 74.39 % 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 (0.34), residues: 583 helix: 0.28 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -2.82 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.021 0.002 TYR B 432 PHE 0.017 0.002 PHE B 343 TRP 0.010 0.002 TRP B 200 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 4853) covalent geometry : angle 0.64915 ( 6563) hydrogen bonds : bond 0.04009 ( 203) hydrogen bonds : angle 4.25013 ( 609) *********************** 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 100 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 369 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8513 (pp) REVERT: B 450 ILE cc_start: 0.7451 (mp) cc_final: 0.6886 (mp) outliers start: 21 outliers final: 15 residues processed: 95 average time/residue: 0.0579 time to fit residues: 7.4175 Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 396 LEU 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 10 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 23 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.176268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158747 restraints weight = 6193.832| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.53 r_work: 0.3871 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4853 Z= 0.113 Angle : 0.581 14.692 6563 Z= 0.284 Chirality : 0.039 0.134 760 Planarity : 0.003 0.044 819 Dihedral : 5.757 53.490 650 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.27 % Allowed : 22.76 % 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 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: -1.00 (0.35), residues: 583 helix: 0.61 (0.30), residues: 344 sheet: None (None), residues: 0 loop : -2.66 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 387 TYR 0.013 0.001 TYR B 209 PHE 0.011 0.001 PHE B 396 TRP 0.015 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4853) covalent geometry : angle 0.58069 ( 6563) hydrogen bonds : bond 0.03357 ( 203) hydrogen bonds : angle 3.94992 ( 609) *********************** 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 103 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8674 (p) cc_final: 0.8328 (p) REVERT: A 118 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: B 369 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 450 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6779 (mp) outliers start: 21 outliers final: 12 residues processed: 96 average time/residue: 0.0552 time to fit residues: 7.3089 Evaluate side-chains 93 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 241 MET 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 241 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.174499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157202 restraints weight = 6288.027| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.62 r_work: 0.3841 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4853 Z= 0.138 Angle : 0.616 14.165 6563 Z= 0.301 Chirality : 0.040 0.119 760 Planarity : 0.003 0.046 819 Dihedral : 5.721 55.700 649 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.25 % Allowed : 23.58 % Favored : 73.17 % 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: -0.98 (0.35), residues: 583 helix: 0.61 (0.29), residues: 346 sheet: None (None), residues: 0 loop : -2.66 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.020 0.001 TYR B 432 PHE 0.014 0.001 PHE B 348 TRP 0.011 0.002 TRP B 200 HIS 0.001 0.000 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4853) covalent geometry : angle 0.61616 ( 6563) hydrogen bonds : bond 0.03623 ( 203) hydrogen bonds : angle 3.99748 ( 609) *********************** 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 97 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8755 (p) cc_final: 0.8382 (p) REVERT: B 369 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 450 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6863 (mp) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.0618 time to fit residues: 7.3714 Evaluate side-chains 92 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 361 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 340 GLU 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 32 optimal weight: 0.7980 chunk 53 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.0570 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.178549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.161216 restraints weight = 6213.347| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.53 r_work: 0.3899 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 4853 Z= 0.107 Angle : 0.580 13.527 6563 Z= 0.284 Chirality : 0.039 0.132 760 Planarity : 0.003 0.046 819 Dihedral : 5.136 54.354 647 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.85 % Allowed : 24.19 % 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 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: -0.69 (0.36), residues: 583 helix: 0.87 (0.30), residues: 348 sheet: None (None), residues: 0 loop : -2.62 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 387 TYR 0.011 0.001 TYR B 209 PHE 0.010 0.001 PHE A 55 TRP 0.017 0.003 TRP B 200 HIS 0.001 0.000 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4853) covalent geometry : angle 0.58030 ( 6563) hydrogen bonds : bond 0.03139 ( 203) hydrogen bonds : angle 3.82777 ( 609) *********************** 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 102 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8648 (p) cc_final: 0.8294 (p) REVERT: B 369 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8449 (pp) REVERT: B 450 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6747 (mp) outliers start: 14 outliers final: 10 residues processed: 96 average time/residue: 0.0626 time to fit residues: 7.9659 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 : 0.209 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 363 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 340 GLU Chi-restraints excluded: chain B residue 369 LEU 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 56 optimal weight: 0.0570 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 49 optimal weight: 0.0170 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 overall best weight: 0.1612 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.180467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.161885 restraints weight = 6192.846| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.72 r_work: 0.3903 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2987 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= 0.102 Angle : 0.572 12.585 6563 Z= 0.280 Chirality : 0.038 0.124 760 Planarity : 0.003 0.048 819 Dihedral : 4.383 53.051 645 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.25 % Allowed : 23.98 % Favored : 72.76 % 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: -0.41 (0.36), residues: 583 helix: 1.06 (0.30), residues: 350 sheet: None (None), residues: 0 loop : -2.47 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.016 0.001 TYR B 432 PHE 0.017 0.001 PHE A 285 TRP 0.018 0.003 TRP B 200 HIS 0.001 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 4853) covalent geometry : angle 0.57217 ( 6563) hydrogen bonds : bond 0.02914 ( 203) hydrogen bonds : angle 3.69005 ( 609) ********************** 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 110 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8717 (p) cc_final: 0.8399 (p) REVERT: A 241 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: B 270 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8018 (mttt) REVERT: B 292 MET cc_start: 0.7958 (ttp) cc_final: 0.7747 (ttt) REVERT: B 369 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8459 (pp) REVERT: B 450 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6834 (mp) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 0.0605 time to fit residues: 8.4073 Evaluate side-chains 98 residues out of total 572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 362 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 315 ILE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 369 LEU 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 29 optimal weight: 0.0470 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.4178 r_free = 0.4178 target = 0.176612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157594 restraints weight = 6294.443| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.75 r_work: 0.3848 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4853 Z= 0.119 Angle : 0.619 15.743 6563 Z= 0.299 Chirality : 0.040 0.119 760 Planarity : 0.003 0.046 819 Dihedral : 4.526 54.913 643 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.44 % Allowed : 25.41 % Favored : 72.15 % 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: -0.35 (0.36), residues: 583 helix: 1.20 (0.30), residues: 345 sheet: None (None), residues: 0 loop : -2.53 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 304 TYR 0.013 0.001 TYR B 209 PHE 0.018 0.001 PHE A 285 TRP 0.012 0.002 TRP B 200 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4853) covalent geometry : angle 0.61875 ( 6563) hydrogen bonds : bond 0.03151 ( 203) hydrogen bonds : angle 3.81636 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.03 seconds wall clock time: 23 minutes 49.51 seconds (1429.51 seconds total)