Starting phenix.real_space_refine on Tue Mar 3 15:42:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esm_28577/03_2026/8esm_28577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esm_28577/03_2026/8esm_28577.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 { model { file = "/net/cci-nas-00/data/ceres_data/8esm_28577/03_2026/8esm_28577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esm_28577/03_2026/8esm_28577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8esm_28577/03_2026/8esm_28577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esm_28577/03_2026/8esm_28577.map" } 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= 0.004 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 42 5.16 5 C 4508 2.51 5 N 1140 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s 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: 6778 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3360 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 18, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'WS0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'WS0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.22, per 1000 atoms: 0.18 Number of scatterers: 6778 At special positions: 0 Unit cell: (112.23, 94.83, 82.65, 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 42 16.00 O 1088 8.00 N 1140 7.00 C 4508 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: 0.48 Conformation dependent library (CDL) restraints added in 174.9 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 87 through 112 removed outlier: 5.768A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.529A pdb=" N GLN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 removed outlier: 3.653A pdb=" N ILE A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 185 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 190 through 226 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.502A pdb=" N ASN A 246 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 247' Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 274 through 300 Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.772A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.575A pdb=" N HIS A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.625A pdb=" N GLN A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.902A pdb=" N ARG A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 420 Processing helix chain 'A' and resid 421 through 424 Processing helix chain 'A' and resid 429 through 447 removed outlier: 4.621A pdb=" N ILE A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 465 through 478 removed outlier: 4.064A pdb=" N VAL A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 112 removed outlier: 5.769A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 removed outlier: 3.530A pdb=" N GLN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 157 removed outlier: 3.653A pdb=" N ILE B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 185 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 190 through 226 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.502A pdb=" N ASN B 246 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 274 through 300 Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.775A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.574A pdb=" N HIS B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 369 through 377 removed outlier: 3.625A pdb=" N GLN B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 376 " --> pdb=" O TYR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 Processing helix chain 'B' and resid 390 through 396 removed outlier: 3.902A pdb=" N ARG B 396 " --> pdb=" O PRO B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 420 Processing helix chain 'B' and resid 421 through 424 Processing helix chain 'B' and resid 429 through 447 removed outlier: 4.621A pdb=" N ILE B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 465 through 478 removed outlier: 4.064A pdb=" N VAL B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1296 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: 0.88 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1894 1.33 - 1.45: 1352 1.45 - 1.57: 3684 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6998 Sorted by residual: bond pdb=" C WS0 B 501 " pdb=" O1 WS0 B 501 " ideal model delta sigma weight residual 1.249 1.310 -0.061 2.00e-02 2.50e+03 9.30e+00 bond pdb=" C WS0 A 501 " pdb=" O1 WS0 A 501 " ideal model delta sigma weight residual 1.249 1.309 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" CA GLN A 297 " pdb=" C GLN A 297 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.72e-02 3.38e+03 5.06e+00 bond pdb=" CA GLN B 297 " pdb=" C GLN B 297 " ideal model delta sigma weight residual 1.522 1.484 0.038 1.72e-02 3.38e+03 4.83e+00 bond pdb=" C WS0 A 501 " pdb=" C1 WS0 A 501 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.23e+00 ... (remaining 6993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 9056 1.60 - 3.19: 371 3.19 - 4.79: 70 4.79 - 6.39: 29 6.39 - 7.99: 4 Bond angle restraints: 9530 Sorted by residual: angle pdb=" N GLY A 464 " pdb=" CA GLY A 464 " pdb=" C GLY A 464 " ideal model delta sigma weight residual 113.18 121.17 -7.99 2.37e+00 1.78e-01 1.14e+01 angle pdb=" N GLY B 464 " pdb=" CA GLY B 464 " pdb=" C GLY B 464 " ideal model delta sigma weight residual 113.18 121.15 -7.97 2.37e+00 1.78e-01 1.13e+01 angle pdb=" CA GLN A 297 " pdb=" C GLN A 297 " pdb=" N GLN A 298 " ideal model delta sigma weight residual 118.59 123.52 -4.93 1.63e+00 3.76e-01 9.16e+00 angle pdb=" N VAL B 478 " pdb=" CA VAL B 478 " pdb=" C VAL B 478 " ideal model delta sigma weight residual 113.07 109.00 4.07 1.36e+00 5.41e-01 8.95e+00 angle pdb=" N VAL A 478 " pdb=" CA VAL A 478 " pdb=" C VAL A 478 " ideal model delta sigma weight residual 113.07 109.00 4.07 1.36e+00 5.41e-01 8.94e+00 ... (remaining 9525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3500 16.26 - 32.51: 451 32.51 - 48.77: 115 48.77 - 65.03: 10 65.03 - 81.29: 6 Dihedral angle restraints: 4082 sinusoidal: 1670 harmonic: 2412 Sorted by residual: dihedral pdb=" CA ILE B 463 " pdb=" C ILE B 463 " pdb=" N GLY B 464 " pdb=" CA GLY B 464 " ideal model delta harmonic sigma weight residual 180.00 160.02 19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ILE A 463 " pdb=" C ILE A 463 " pdb=" N GLY A 464 " pdb=" CA GLY A 464 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TYR B 253 " pdb=" C TYR B 253 " pdb=" N TYR B 254 " pdb=" CA TYR B 254 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 516 0.030 - 0.059: 314 0.059 - 0.088: 131 0.088 - 0.118: 63 0.118 - 0.147: 8 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CA ARG B 387 " pdb=" N ARG B 387 " pdb=" C ARG B 387 " pdb=" CB ARG B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ARG A 387 " pdb=" N ARG A 387 " pdb=" C ARG A 387 " pdb=" CB ARG A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA GLN B 297 " pdb=" N GLN B 297 " pdb=" C GLN B 297 " pdb=" CB GLN B 297 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1029 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 WS0 B 501 " 0.109 2.00e-02 2.50e+03 6.38e-02 8.14e+01 pdb=" C18 WS0 B 501 " -0.042 2.00e-02 2.50e+03 pdb=" C19 WS0 B 501 " -0.044 2.00e-02 2.50e+03 pdb=" C5 WS0 B 501 " 0.110 2.00e-02 2.50e+03 pdb=" C6 WS0 B 501 " -0.025 2.00e-02 2.50e+03 pdb=" C7 WS0 B 501 " -0.045 2.00e-02 2.50e+03 pdb=" C8 WS0 B 501 " -0.042 2.00e-02 2.50e+03 pdb=" C9 WS0 B 501 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 WS0 A 501 " -0.103 2.00e-02 2.50e+03 6.09e-02 7.43e+01 pdb=" C18 WS0 A 501 " 0.039 2.00e-02 2.50e+03 pdb=" C19 WS0 A 501 " 0.044 2.00e-02 2.50e+03 pdb=" C5 WS0 A 501 " -0.106 2.00e-02 2.50e+03 pdb=" C6 WS0 A 501 " 0.025 2.00e-02 2.50e+03 pdb=" C7 WS0 A 501 " 0.043 2.00e-02 2.50e+03 pdb=" C8 WS0 A 501 " 0.039 2.00e-02 2.50e+03 pdb=" C9 WS0 A 501 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WS0 B 501 " -0.082 2.00e-02 2.50e+03 4.71e-02 4.99e+01 pdb=" C11 WS0 B 501 " -0.008 2.00e-02 2.50e+03 pdb=" C12 WS0 B 501 " 0.014 2.00e-02 2.50e+03 pdb=" C13 WS0 B 501 " -0.029 2.00e-02 2.50e+03 pdb=" C14 WS0 B 501 " -0.008 2.00e-02 2.50e+03 pdb=" N1 WS0 B 501 " 0.056 2.00e-02 2.50e+03 pdb=" N2 WS0 B 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 WS0 B 501 " -0.033 2.00e-02 2.50e+03 pdb=" O2 WS0 B 501 " 0.088 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 191 2.69 - 3.24: 6942 3.24 - 3.80: 11132 3.80 - 4.35: 13496 4.35 - 4.90: 23149 Nonbonded interactions: 54910 Sorted by model distance: nonbonded pdb=" OE2 GLU B 284 " pdb=" OH TYR B 339 " model vdw 2.141 3.040 nonbonded pdb=" OE2 GLU A 284 " pdb=" OH TYR A 339 " model vdw 2.141 3.040 nonbonded pdb=" OG SER A 210 " pdb=" NE2 HIS A 388 " model vdw 2.240 3.120 nonbonded pdb=" OG SER B 210 " pdb=" NE2 HIS B 388 " model vdw 2.240 3.120 nonbonded pdb=" O SER A 399 " pdb=" N MET A 402 " model vdw 2.244 3.120 ... (remaining 54905 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.170 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: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 6998 Z= 0.397 Angle : 0.815 7.986 9530 Z= 0.429 Chirality : 0.046 0.147 1032 Planarity : 0.006 0.064 1166 Dihedral : 14.890 81.285 2518 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.56 % Allowed : 10.64 % Favored : 88.80 % 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: -2.85 (0.26), residues: 804 helix: -1.19 (0.19), residues: 604 sheet: None (None), residues: 0 loop : -3.75 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 220 TYR 0.015 0.002 TYR B 417 PHE 0.014 0.002 PHE B 277 TRP 0.009 0.002 TRP A 299 HIS 0.006 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00937 ( 6998) covalent geometry : angle 0.81466 ( 9530) hydrogen bonds : bond 0.08933 ( 434) hydrogen bonds : angle 5.76607 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.213 Fit side-chains REVERT: A 131 TRP cc_start: 0.7103 (m100) cc_final: 0.6472 (m100) REVERT: A 151 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7966 (mm-30) REVERT: A 318 ARG cc_start: 0.6589 (mmp80) cc_final: 0.5597 (mmp-170) REVERT: A 389 PHE cc_start: 0.8804 (t80) cc_final: 0.8520 (t80) REVERT: B 131 TRP cc_start: 0.7146 (m100) cc_final: 0.6504 (m100) REVERT: B 151 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 284 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 318 ARG cc_start: 0.6580 (mmp80) cc_final: 0.5593 (mmp-170) REVERT: B 389 PHE cc_start: 0.8821 (t80) cc_final: 0.8562 (t80) REVERT: B 426 PHE cc_start: 0.8102 (m-80) cc_final: 0.7876 (m-80) REVERT: B 427 ARG cc_start: 0.8194 (mpt90) cc_final: 0.7854 (mpt180) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.1347 time to fit residues: 21.5956 Evaluate side-chains 101 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain B residue 130 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 306 ASN ** A 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 306 ASN ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112413 restraints weight = 8911.300| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.21 r_work: 0.3033 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6998 Z= 0.135 Angle : 0.611 7.808 9530 Z= 0.299 Chirality : 0.038 0.111 1032 Planarity : 0.005 0.036 1166 Dihedral : 6.019 32.340 976 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.84 % Allowed : 12.89 % Favored : 86.27 % 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: -0.82 (0.30), residues: 804 helix: 0.37 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.41 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.015 0.001 TYR B 211 PHE 0.015 0.001 PHE A 277 TRP 0.007 0.001 TRP B 91 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6998) covalent geometry : angle 0.61115 ( 9530) hydrogen bonds : bond 0.03973 ( 434) hydrogen bonds : angle 4.78385 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.250 Fit side-chains REVERT: A 131 TRP cc_start: 0.6681 (m100) cc_final: 0.6098 (m-10) REVERT: A 353 MET cc_start: 0.8596 (ptm) cc_final: 0.8246 (ptp) REVERT: A 389 PHE cc_start: 0.9008 (t80) cc_final: 0.8471 (t80) REVERT: A 426 PHE cc_start: 0.8155 (m-80) cc_final: 0.7938 (m-80) REVERT: A 431 PHE cc_start: 0.8835 (t80) cc_final: 0.8554 (t80) REVERT: A 477 TYR cc_start: 0.8563 (t80) cc_final: 0.7766 (t80) REVERT: B 151 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7950 (mm-30) REVERT: B 353 MET cc_start: 0.8569 (ptm) cc_final: 0.8188 (ptp) REVERT: B 389 PHE cc_start: 0.9033 (t80) cc_final: 0.8499 (t80) REVERT: B 426 PHE cc_start: 0.8149 (m-80) cc_final: 0.7941 (m-80) REVERT: B 477 TYR cc_start: 0.8609 (t80) cc_final: 0.7882 (t80) outliers start: 6 outliers final: 2 residues processed: 114 average time/residue: 0.0655 time to fit residues: 10.2620 Evaluate side-chains 102 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS B 382 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110100 restraints weight = 8895.536| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.18 r_work: 0.2979 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6998 Z= 0.185 Angle : 0.606 7.661 9530 Z= 0.300 Chirality : 0.039 0.111 1032 Planarity : 0.005 0.036 1166 Dihedral : 5.536 31.683 974 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 1.68 % Allowed : 14.99 % Favored : 83.33 % 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: -0.30 (0.30), residues: 804 helix: 0.74 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.21 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.016 0.001 TYR B 417 PHE 0.016 0.002 PHE A 277 TRP 0.006 0.001 TRP A 365 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6998) covalent geometry : angle 0.60587 ( 9530) hydrogen bonds : bond 0.04078 ( 434) hydrogen bonds : angle 4.75876 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.224 Fit side-chains REVERT: A 161 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 353 MET cc_start: 0.8666 (ptm) cc_final: 0.8265 (ptp) REVERT: A 389 PHE cc_start: 0.9030 (t80) cc_final: 0.8464 (t80) REVERT: A 431 PHE cc_start: 0.8841 (t80) cc_final: 0.8607 (t80) REVERT: A 477 TYR cc_start: 0.8556 (t80) cc_final: 0.7817 (t80) REVERT: B 79 ASP cc_start: 0.8559 (p0) cc_final: 0.8355 (p0) REVERT: B 151 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8020 (mm-30) REVERT: B 353 MET cc_start: 0.8633 (ptm) cc_final: 0.8218 (ptp) REVERT: B 389 PHE cc_start: 0.9056 (t80) cc_final: 0.8487 (t80) REVERT: B 477 TYR cc_start: 0.8583 (t80) cc_final: 0.7820 (t80) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.0769 time to fit residues: 11.7999 Evaluate side-chains 113 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106140 restraints weight = 8971.034| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.04 r_work: 0.2998 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6998 Z= 0.184 Angle : 0.599 7.572 9530 Z= 0.295 Chirality : 0.039 0.111 1032 Planarity : 0.005 0.038 1166 Dihedral : 5.381 32.133 974 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 1.26 % Allowed : 17.37 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.31), residues: 804 helix: 1.00 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.06 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.016 0.001 TYR B 417 PHE 0.012 0.001 PHE A 277 TRP 0.005 0.001 TRP A 334 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6998) covalent geometry : angle 0.59851 ( 9530) hydrogen bonds : bond 0.04028 ( 434) hydrogen bonds : angle 4.71679 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.250 Fit side-chains REVERT: A 67 ARG cc_start: 0.7427 (mmm-85) cc_final: 0.6996 (mmm-85) REVERT: A 389 PHE cc_start: 0.9135 (t80) cc_final: 0.8528 (t80) REVERT: A 402 MET cc_start: 0.7873 (tpp) cc_final: 0.7492 (tmm) REVERT: A 477 TYR cc_start: 0.8591 (t80) cc_final: 0.7836 (t80) REVERT: B 389 PHE cc_start: 0.9137 (t80) cc_final: 0.8535 (t80) REVERT: B 402 MET cc_start: 0.7857 (tpp) cc_final: 0.7483 (tmm) REVERT: B 477 TYR cc_start: 0.8649 (t80) cc_final: 0.7878 (t80) outliers start: 9 outliers final: 6 residues processed: 116 average time/residue: 0.0752 time to fit residues: 11.8247 Evaluate side-chains 111 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.114985 restraints weight = 8901.696| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.24 r_work: 0.3064 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.002 0.024 6998 Z= 0.112 Angle : 0.542 7.545 9530 Z= 0.266 Chirality : 0.037 0.110 1032 Planarity : 0.004 0.039 1166 Dihedral : 4.718 27.533 974 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.26 % Allowed : 17.51 % Favored : 81.23 % 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: 0.70 (0.32), residues: 804 helix: 1.44 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.98 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.016 0.001 TYR B 417 PHE 0.011 0.001 PHE A 277 TRP 0.007 0.001 TRP B 131 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6998) covalent geometry : angle 0.54200 ( 9530) hydrogen bonds : bond 0.03367 ( 434) hydrogen bonds : angle 4.54377 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.244 Fit side-chains REVERT: A 213 ASP cc_start: 0.9027 (m-30) cc_final: 0.8767 (m-30) REVERT: A 389 PHE cc_start: 0.8961 (t80) cc_final: 0.8363 (t80) REVERT: A 402 MET cc_start: 0.7714 (tpp) cc_final: 0.7399 (tmm) REVERT: A 477 TYR cc_start: 0.8498 (t80) cc_final: 0.7640 (t80) REVERT: B 315 ASP cc_start: 0.6454 (p0) cc_final: 0.6171 (p0) REVERT: B 389 PHE cc_start: 0.8962 (t80) cc_final: 0.8374 (t80) REVERT: B 402 MET cc_start: 0.7715 (tpp) cc_final: 0.7407 (tmm) REVERT: B 477 TYR cc_start: 0.8526 (t80) cc_final: 0.7646 (t80) outliers start: 9 outliers final: 8 residues processed: 124 average time/residue: 0.0852 time to fit residues: 13.9623 Evaluate side-chains 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.107283 restraints weight = 9063.117| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.07 r_work: 0.3030 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6998 Z= 0.167 Angle : 0.583 7.284 9530 Z= 0.287 Chirality : 0.039 0.111 1032 Planarity : 0.004 0.038 1166 Dihedral : 5.074 31.255 974 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.82 % Allowed : 18.21 % Favored : 79.97 % 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: 0.60 (0.31), residues: 804 helix: 1.40 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.92 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.015 0.001 TYR B 417 PHE 0.010 0.001 PHE B 277 TRP 0.005 0.001 TRP A 334 HIS 0.002 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6998) covalent geometry : angle 0.58325 ( 9530) hydrogen bonds : bond 0.03767 ( 434) hydrogen bonds : angle 4.63171 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.209 Fit side-chains REVERT: A 315 ASP cc_start: 0.6647 (p0) cc_final: 0.6387 (p0) REVERT: A 389 PHE cc_start: 0.9117 (t80) cc_final: 0.8498 (t80) REVERT: A 402 MET cc_start: 0.7880 (tpp) cc_final: 0.7448 (tmm) REVERT: A 477 TYR cc_start: 0.8600 (t80) cc_final: 0.7752 (t80) REVERT: B 315 ASP cc_start: 0.6631 (p0) cc_final: 0.6356 (p0) REVERT: B 389 PHE cc_start: 0.9127 (t80) cc_final: 0.8483 (t80) REVERT: B 402 MET cc_start: 0.7922 (tpp) cc_final: 0.7488 (tmm) REVERT: B 477 TYR cc_start: 0.8622 (t80) cc_final: 0.7749 (t80) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.0797 time to fit residues: 12.9696 Evaluate side-chains 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111717 restraints weight = 8932.403| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.27 r_work: 0.3012 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6998 Z= 0.156 Angle : 0.571 7.193 9530 Z= 0.281 Chirality : 0.038 0.111 1032 Planarity : 0.004 0.038 1166 Dihedral : 5.003 30.322 974 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.10 % Allowed : 18.49 % Favored : 79.41 % 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: 0.67 (0.31), residues: 804 helix: 1.45 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.91 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.016 0.001 TYR B 417 PHE 0.011 0.001 PHE B 277 TRP 0.005 0.001 TRP A 334 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6998) covalent geometry : angle 0.57144 ( 9530) hydrogen bonds : bond 0.03700 ( 434) hydrogen bonds : angle 4.60769 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.228 Fit side-chains REVERT: A 315 ASP cc_start: 0.6646 (p0) cc_final: 0.6358 (p0) REVERT: A 389 PHE cc_start: 0.8999 (t80) cc_final: 0.8380 (t80) REVERT: A 402 MET cc_start: 0.7793 (tpp) cc_final: 0.7443 (tmm) REVERT: A 446 ARG cc_start: 0.7349 (ttt90) cc_final: 0.7008 (tpp80) REVERT: A 477 TYR cc_start: 0.8540 (t80) cc_final: 0.7657 (t80) REVERT: B 315 ASP cc_start: 0.6604 (p0) cc_final: 0.6340 (p0) REVERT: B 389 PHE cc_start: 0.8995 (t80) cc_final: 0.8412 (t80) REVERT: B 402 MET cc_start: 0.7796 (tpp) cc_final: 0.7426 (tmm) REVERT: B 446 ARG cc_start: 0.7345 (ttt90) cc_final: 0.6997 (tpp80) REVERT: B 477 TYR cc_start: 0.8557 (t80) cc_final: 0.7659 (t80) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.0870 time to fit residues: 14.5024 Evaluate side-chains 123 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111049 restraints weight = 9013.979| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.08 r_work: 0.3065 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6998 Z= 0.112 Angle : 0.544 7.131 9530 Z= 0.266 Chirality : 0.037 0.110 1032 Planarity : 0.004 0.039 1166 Dihedral : 4.684 28.340 974 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.68 % Allowed : 18.91 % Favored : 79.41 % 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: 1.05 (0.32), residues: 804 helix: 1.67 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.78 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.017 0.001 TYR B 417 PHE 0.011 0.001 PHE B 277 TRP 0.005 0.001 TRP A 334 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6998) covalent geometry : angle 0.54380 ( 9530) hydrogen bonds : bond 0.03318 ( 434) hydrogen bonds : angle 4.51154 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.299 Fit side-chains REVERT: A 315 ASP cc_start: 0.6695 (p0) cc_final: 0.6403 (p0) REVERT: A 402 MET cc_start: 0.7771 (tpp) cc_final: 0.7305 (tmm) REVERT: A 446 ARG cc_start: 0.7378 (ttt90) cc_final: 0.7058 (tpp80) REVERT: A 477 TYR cc_start: 0.8580 (t80) cc_final: 0.7738 (t80) REVERT: B 315 ASP cc_start: 0.6628 (p0) cc_final: 0.6359 (p0) REVERT: B 389 PHE cc_start: 0.9067 (t80) cc_final: 0.8430 (t80) REVERT: B 402 MET cc_start: 0.7763 (tpp) cc_final: 0.7343 (tmm) REVERT: B 446 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7090 (tpp80) REVERT: B 477 TYR cc_start: 0.8588 (t80) cc_final: 0.7737 (t80) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.0819 time to fit residues: 13.5090 Evaluate side-chains 124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.0020 chunk 1 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 0.0070 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 52 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.152547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116898 restraints weight = 8906.931| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.09 r_work: 0.3157 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6998 Z= 0.097 Angle : 0.532 8.724 9530 Z= 0.261 Chirality : 0.036 0.134 1032 Planarity : 0.004 0.041 1166 Dihedral : 4.276 25.322 974 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.26 % Allowed : 19.33 % Favored : 79.41 % 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: 1.31 (0.32), residues: 804 helix: 1.91 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -2.87 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.017 0.001 TYR B 417 PHE 0.025 0.001 PHE A 148 TRP 0.007 0.001 TRP B 334 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 6998) covalent geometry : angle 0.53232 ( 9530) hydrogen bonds : bond 0.02903 ( 434) hydrogen bonds : angle 4.38196 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.177 Fit side-chains REVERT: A 315 ASP cc_start: 0.6655 (p0) cc_final: 0.6350 (p0) REVERT: A 389 PHE cc_start: 0.8587 (t80) cc_final: 0.8352 (t80) REVERT: A 402 MET cc_start: 0.7655 (tpp) cc_final: 0.7329 (tmm) REVERT: A 426 PHE cc_start: 0.8252 (m-80) cc_final: 0.7381 (t80) REVERT: A 446 ARG cc_start: 0.7437 (ttt90) cc_final: 0.7118 (tpp80) REVERT: A 477 TYR cc_start: 0.8597 (t80) cc_final: 0.7620 (t80) REVERT: B 315 ASP cc_start: 0.6619 (p0) cc_final: 0.6286 (p0) REVERT: B 402 MET cc_start: 0.7692 (tpp) cc_final: 0.7348 (tmm) REVERT: B 426 PHE cc_start: 0.8225 (m-80) cc_final: 0.7378 (t80) REVERT: B 446 ARG cc_start: 0.7453 (ttt90) cc_final: 0.7107 (tpp80) REVERT: B 477 TYR cc_start: 0.8592 (t80) cc_final: 0.7671 (t80) outliers start: 9 outliers final: 7 residues processed: 134 average time/residue: 0.0842 time to fit residues: 14.7897 Evaluate side-chains 120 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 0.0070 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.148175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115720 restraints weight = 8951.776| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.22 r_work: 0.3066 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6998 Z= 0.129 Angle : 0.563 8.332 9530 Z= 0.275 Chirality : 0.038 0.112 1032 Planarity : 0.004 0.038 1166 Dihedral : 4.589 29.069 974 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.12 % Allowed : 19.33 % Favored : 79.55 % 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: 1.29 (0.32), residues: 804 helix: 1.88 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.88 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 67 TYR 0.017 0.001 TYR B 417 PHE 0.023 0.001 PHE B 148 TRP 0.006 0.001 TRP A 384 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6998) covalent geometry : angle 0.56264 ( 9530) hydrogen bonds : bond 0.03198 ( 434) hydrogen bonds : angle 4.44020 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.245 Fit side-chains REVERT: A 315 ASP cc_start: 0.6690 (p0) cc_final: 0.6379 (p0) REVERT: A 402 MET cc_start: 0.7654 (tpp) cc_final: 0.7400 (tmm) REVERT: A 446 ARG cc_start: 0.7361 (ttt90) cc_final: 0.7053 (tpp80) REVERT: A 477 TYR cc_start: 0.8514 (t80) cc_final: 0.7614 (t80) REVERT: B 315 ASP cc_start: 0.6601 (p0) cc_final: 0.6280 (p0) REVERT: B 389 PHE cc_start: 0.8823 (t80) cc_final: 0.8587 (t80) REVERT: B 402 MET cc_start: 0.7689 (tpp) cc_final: 0.7297 (tmm) REVERT: B 446 ARG cc_start: 0.7367 (ttt90) cc_final: 0.7032 (tpp80) REVERT: B 477 TYR cc_start: 0.8525 (t80) cc_final: 0.7617 (t80) outliers start: 8 outliers final: 8 residues processed: 126 average time/residue: 0.0944 time to fit residues: 15.4631 Evaluate side-chains 125 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 0.0670 chunk 68 optimal weight: 0.3980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.113468 restraints weight = 8879.952| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.08 r_work: 0.3108 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6998 Z= 0.108 Angle : 0.555 7.617 9530 Z= 0.271 Chirality : 0.039 0.188 1032 Planarity : 0.004 0.039 1166 Dihedral : 4.485 28.066 974 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.98 % Allowed : 19.89 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.32), residues: 804 helix: 1.93 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.86 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 67 TYR 0.017 0.001 TYR B 417 PHE 0.022 0.001 PHE B 148 TRP 0.005 0.001 TRP A 374 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 6998) covalent geometry : angle 0.55480 ( 9530) hydrogen bonds : bond 0.03125 ( 434) hydrogen bonds : angle 4.42748 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1761.54 seconds wall clock time: 30 minutes 45.39 seconds (1845.39 seconds total)