Starting phenix.real_space_refine on Thu Jul 24 22:17:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esm_28577/07_2025/8esm_28577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esm_28577/07_2025/8esm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8esm_28577/07_2025/8esm_28577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esm_28577/07_2025/8esm_28577.map" model { file = "/net/cci-nas-00/data/ceres_data/8esm_28577/07_2025/8esm_28577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esm_28577/07_2025/8esm_28577.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.30, per 1000 atoms: 0.63 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: 1.54 Conformation dependent library (CDL) restraints added in 866.4 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: 0.53 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: 1.64 Time building geometry restraints manager: 1.84 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: 0.03 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (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 TRP 0.009 0.002 TRP A 299 HIS 0.006 0.001 HIS B 382 PHE 0.014 0.002 PHE B 277 TYR 0.015 0.002 TYR B 417 ARG 0.003 0.000 ARG B 220 Details of bonding type rmsd hydrogen bonds : bond 0.08933 ( 434) hydrogen bonds : angle 5.76607 ( 1296) covalent geometry : bond 0.00937 ( 6998) covalent geometry : angle 0.81466 ( 9530) *********************** 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 : 0.766 Fit side-chains REVERT: A 131 TRP cc_start: 0.7103 (m100) cc_final: 0.6471 (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: 0.3297 time to fit residues: 53.4027 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 : 0.719 ------------------------------------------------------------------------------- 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 67 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 B 162 GLN B 292 GLN B 306 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113351 restraints weight = 8695.376| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.11 r_work: 0.3052 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1423 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= 0.130 Angle : 0.607 7.912 9530 Z= 0.298 Chirality : 0.038 0.116 1032 Planarity : 0.005 0.035 1166 Dihedral : 5.818 30.550 976 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.84 % Allowed : 13.73 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.30), residues: 804 helix: 0.43 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.40 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 91 HIS 0.003 0.001 HIS B 201 PHE 0.015 0.001 PHE A 277 TYR 0.015 0.001 TYR B 211 ARG 0.003 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 434) hydrogen bonds : angle 4.75524 ( 1296) covalent geometry : bond 0.00279 ( 6998) covalent geometry : angle 0.60677 ( 9530) *********************** 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 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.682 Fit side-chains REVERT: A 131 TRP cc_start: 0.6685 (m100) cc_final: 0.6049 (m-10) REVERT: A 353 MET cc_start: 0.8676 (ptm) cc_final: 0.8307 (ptp) REVERT: A 389 PHE cc_start: 0.9116 (t80) cc_final: 0.8526 (t80) REVERT: A 426 PHE cc_start: 0.8277 (m-80) cc_final: 0.8066 (m-80) REVERT: A 431 PHE cc_start: 0.8832 (t80) cc_final: 0.8500 (t80) REVERT: A 477 TYR cc_start: 0.8633 (t80) cc_final: 0.7874 (t80) REVERT: B 151 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 353 MET cc_start: 0.8661 (ptm) cc_final: 0.8279 (ptp) REVERT: B 389 PHE cc_start: 0.9120 (t80) cc_final: 0.8547 (t80) REVERT: B 426 PHE cc_start: 0.8246 (m-80) cc_final: 0.8045 (m-80) REVERT: B 431 PHE cc_start: 0.8822 (t80) cc_final: 0.8487 (t80) REVERT: B 477 TYR cc_start: 0.8673 (t80) cc_final: 0.7961 (t80) outliers start: 6 outliers final: 3 residues processed: 116 average time/residue: 0.1891 time to fit residues: 29.5261 Evaluate side-chains 105 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- 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 = 0.143646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.107724 restraints weight = 8932.732| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.05 r_work: 0.3036 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6998 Z= 0.150 Angle : 0.581 7.436 9530 Z= 0.287 Chirality : 0.038 0.110 1032 Planarity : 0.005 0.036 1166 Dihedral : 5.303 30.572 974 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 1.12 % Allowed : 15.41 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.31), residues: 804 helix: 0.87 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.20 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.003 0.001 HIS B 201 PHE 0.016 0.001 PHE A 277 TYR 0.016 0.001 TYR B 417 ARG 0.002 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 434) hydrogen bonds : angle 4.67715 ( 1296) covalent geometry : bond 0.00344 ( 6998) covalent geometry : angle 0.58107 ( 9530) *********************** 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 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.866 Fit side-chains REVERT: A 161 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7822 (mm-30) REVERT: A 389 PHE cc_start: 0.9123 (t80) cc_final: 0.8530 (t80) REVERT: A 402 MET cc_start: 0.7766 (tpp) cc_final: 0.7370 (tmm) REVERT: A 431 PHE cc_start: 0.8863 (t80) cc_final: 0.8621 (t80) REVERT: A 477 TYR cc_start: 0.8668 (t80) cc_final: 0.7955 (t80) REVERT: B 151 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8060 (mm-30) REVERT: B 389 PHE cc_start: 0.9130 (t80) cc_final: 0.8555 (t80) REVERT: B 431 PHE cc_start: 0.8858 (t80) cc_final: 0.8602 (t80) REVERT: B 477 TYR cc_start: 0.8708 (t80) cc_final: 0.7958 (t80) outliers start: 8 outliers final: 6 residues processed: 118 average time/residue: 0.1850 time to fit residues: 29.4904 Evaluate side-chains 114 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.143065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110874 restraints weight = 8987.380| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.22 r_work: 0.2990 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1822 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 7.368 9530 Z= 0.288 Chirality : 0.039 0.110 1032 Planarity : 0.004 0.037 1166 Dihedral : 5.233 31.309 974 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.40 % Allowed : 15.69 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.31), residues: 804 helix: 1.06 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.06 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.001 PHE A 277 TYR 0.016 0.001 TYR B 417 ARG 0.002 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 434) hydrogen bonds : angle 4.67268 ( 1296) covalent geometry : bond 0.00391 ( 6998) covalent geometry : angle 0.58260 ( 9530) *********************** 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 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.684 Fit side-chains REVERT: A 67 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6819 (mmm-85) REVERT: A 389 PHE cc_start: 0.9015 (t80) cc_final: 0.8411 (t80) REVERT: A 402 MET cc_start: 0.7664 (tpp) cc_final: 0.7353 (tmm) REVERT: A 431 PHE cc_start: 0.8819 (t80) cc_final: 0.8579 (t80) REVERT: A 477 TYR cc_start: 0.8554 (t80) cc_final: 0.7767 (t80) REVERT: B 353 MET cc_start: 0.8603 (ptm) cc_final: 0.8178 (ptp) REVERT: B 389 PHE cc_start: 0.9022 (t80) cc_final: 0.8437 (t80) REVERT: B 402 MET cc_start: 0.7763 (tpp) cc_final: 0.7479 (tmm) REVERT: B 431 PHE cc_start: 0.8812 (t80) cc_final: 0.8555 (t80) REVERT: B 477 TYR cc_start: 0.8583 (t80) cc_final: 0.7800 (t80) outliers start: 10 outliers final: 8 residues processed: 119 average time/residue: 0.1879 time to fit residues: 30.0992 Evaluate side-chains 114 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.145494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113571 restraints weight = 8876.034| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.18 r_work: 0.3046 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6998 Z= 0.124 Angle : 0.556 7.065 9530 Z= 0.272 Chirality : 0.037 0.110 1032 Planarity : 0.004 0.038 1166 Dihedral : 4.901 29.190 974 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.31), residues: 804 helix: 1.35 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.97 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 334 HIS 0.002 0.001 HIS A 201 PHE 0.011 0.001 PHE A 277 TYR 0.016 0.001 TYR B 417 ARG 0.002 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 434) hydrogen bonds : angle 4.56737 ( 1296) covalent geometry : bond 0.00278 ( 6998) covalent geometry : angle 0.55599 ( 9530) *********************** 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 122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.696 Fit side-chains REVERT: A 67 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6847 (mmm-85) REVERT: A 389 PHE cc_start: 0.8984 (t80) cc_final: 0.8381 (t80) REVERT: A 402 MET cc_start: 0.7625 (tpp) cc_final: 0.7288 (tmm) REVERT: A 431 PHE cc_start: 0.8784 (t80) cc_final: 0.8501 (t80) REVERT: A 477 TYR cc_start: 0.8524 (t80) cc_final: 0.7666 (t80) REVERT: B 315 ASP cc_start: 0.6478 (p0) cc_final: 0.6186 (p0) REVERT: B 389 PHE cc_start: 0.8985 (t80) cc_final: 0.8388 (t80) REVERT: B 402 MET cc_start: 0.7758 (tpp) cc_final: 0.7442 (tmm) REVERT: B 431 PHE cc_start: 0.8775 (t80) cc_final: 0.8498 (t80) REVERT: B 477 TYR cc_start: 0.8539 (t80) cc_final: 0.7743 (t80) outliers start: 9 outliers final: 8 residues processed: 119 average time/residue: 0.1992 time to fit residues: 31.2141 Evaluate side-chains 117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 49 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.147329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111359 restraints weight = 8904.379| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.07 r_work: 0.3084 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2307 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 : 0.536 6.787 9530 Z= 0.264 Chirality : 0.037 0.109 1032 Planarity : 0.004 0.039 1166 Dihedral : 4.667 28.714 974 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.26 % Allowed : 17.79 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.32), residues: 804 helix: 1.64 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.87 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 334 HIS 0.002 0.000 HIS A 201 PHE 0.010 0.001 PHE B 277 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 434) hydrogen bonds : angle 4.48007 ( 1296) covalent geometry : bond 0.00245 ( 6998) covalent geometry : angle 0.53593 ( 9530) *********************** 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 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.736 Fit side-chains REVERT: A 315 ASP cc_start: 0.6660 (p0) cc_final: 0.6332 (p0) REVERT: A 402 MET cc_start: 0.7748 (tpp) cc_final: 0.7262 (tmm) REVERT: A 431 PHE cc_start: 0.8817 (t80) cc_final: 0.8554 (t80) REVERT: A 446 ARG cc_start: 0.7416 (ttt90) cc_final: 0.7053 (tpp80) REVERT: A 477 TYR cc_start: 0.8588 (t80) cc_final: 0.7718 (t80) REVERT: B 315 ASP cc_start: 0.6595 (p0) cc_final: 0.6303 (p0) REVERT: B 389 PHE cc_start: 0.9044 (t80) cc_final: 0.8450 (t80) REVERT: B 402 MET cc_start: 0.7810 (tpp) cc_final: 0.7402 (tmm) REVERT: B 431 PHE cc_start: 0.8822 (t80) cc_final: 0.8581 (t80) REVERT: B 477 TYR cc_start: 0.8611 (t80) cc_final: 0.7719 (t80) outliers start: 9 outliers final: 8 residues processed: 125 average time/residue: 0.2038 time to fit residues: 33.3106 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.146204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110297 restraints weight = 8871.643| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.06 r_work: 0.3065 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6998 Z= 0.131 Angle : 0.556 6.859 9530 Z= 0.272 Chirality : 0.038 0.131 1032 Planarity : 0.004 0.037 1166 Dihedral : 4.786 30.065 974 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.68 % Allowed : 18.49 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.31), residues: 804 helix: 1.63 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.85 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 384 HIS 0.002 0.001 HIS B 201 PHE 0.018 0.001 PHE B 148 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 434) hydrogen bonds : angle 4.52056 ( 1296) covalent geometry : bond 0.00298 ( 6998) covalent geometry : angle 0.55592 ( 9530) *********************** 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 125 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.774 Fit side-chains REVERT: A 315 ASP cc_start: 0.6670 (p0) cc_final: 0.6394 (p0) REVERT: A 402 MET cc_start: 0.7762 (tpp) cc_final: 0.7226 (tmm) REVERT: A 431 PHE cc_start: 0.8866 (t80) cc_final: 0.8594 (t80) REVERT: A 477 TYR cc_start: 0.8602 (t80) cc_final: 0.7734 (t80) REVERT: B 315 ASP cc_start: 0.6544 (p0) cc_final: 0.6260 (p0) REVERT: B 389 PHE cc_start: 0.9064 (t80) cc_final: 0.8398 (t80) REVERT: B 402 MET cc_start: 0.7806 (tpp) cc_final: 0.7394 (tmm) REVERT: B 431 PHE cc_start: 0.8867 (t80) cc_final: 0.8610 (t80) REVERT: B 477 TYR cc_start: 0.8610 (t80) cc_final: 0.7737 (t80) outliers start: 12 outliers final: 9 residues processed: 123 average time/residue: 0.2051 time to fit residues: 33.0988 Evaluate side-chains 122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.147491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111383 restraints weight = 8929.666| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.08 r_work: 0.3081 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6998 Z= 0.116 Angle : 0.545 6.790 9530 Z= 0.267 Chirality : 0.037 0.115 1032 Planarity : 0.004 0.038 1166 Dihedral : 4.647 29.127 974 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.40 % Allowed : 18.35 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.32), residues: 804 helix: 1.71 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.83 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.002 0.000 HIS A 201 PHE 0.014 0.001 PHE B 148 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 434) hydrogen bonds : angle 4.48232 ( 1296) covalent geometry : bond 0.00255 ( 6998) covalent geometry : angle 0.54454 ( 9530) *********************** 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 125 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.767 Fit side-chains REVERT: A 67 ARG cc_start: 0.7321 (mmm-85) cc_final: 0.6991 (mmm-85) REVERT: A 315 ASP cc_start: 0.6658 (p0) cc_final: 0.6386 (p0) REVERT: A 389 PHE cc_start: 0.8995 (t80) cc_final: 0.8700 (t80) REVERT: A 402 MET cc_start: 0.7746 (tpp) cc_final: 0.7261 (tmm) REVERT: A 431 PHE cc_start: 0.8857 (t80) cc_final: 0.8603 (t80) REVERT: A 446 ARG cc_start: 0.7426 (ttt90) cc_final: 0.7081 (tpp80) REVERT: A 477 TYR cc_start: 0.8604 (t80) cc_final: 0.7653 (t80) REVERT: B 315 ASP cc_start: 0.6557 (p0) cc_final: 0.6258 (p0) REVERT: B 402 MET cc_start: 0.7827 (tpp) cc_final: 0.7333 (tmm) REVERT: B 431 PHE cc_start: 0.8853 (t80) cc_final: 0.8608 (t80) REVERT: B 477 TYR cc_start: 0.8614 (t80) cc_final: 0.7727 (t80) outliers start: 10 outliers final: 9 residues processed: 123 average time/residue: 0.2045 time to fit residues: 33.0031 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 50 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.148429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116546 restraints weight = 8898.030| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.23 r_work: 0.3082 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6998 Z= 0.107 Angle : 0.537 6.618 9530 Z= 0.263 Chirality : 0.037 0.110 1032 Planarity : 0.004 0.038 1166 Dihedral : 4.541 28.334 974 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.26 % Allowed : 18.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.32), residues: 804 helix: 1.81 (0.22), residues: 618 sheet: None (None), residues: 0 loop : -2.89 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 334 HIS 0.002 0.000 HIS A 201 PHE 0.013 0.001 PHE B 148 TYR 0.017 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 434) hydrogen bonds : angle 4.44482 ( 1296) covalent geometry : bond 0.00232 ( 6998) covalent geometry : angle 0.53686 ( 9530) *********************** 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 125 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.775 Fit side-chains REVERT: A 315 ASP cc_start: 0.6590 (p0) cc_final: 0.6318 (p0) REVERT: A 402 MET cc_start: 0.7617 (tpp) cc_final: 0.7318 (tmm) REVERT: A 431 PHE cc_start: 0.8818 (t80) cc_final: 0.8609 (t80) REVERT: A 446 ARG cc_start: 0.7353 (ttt90) cc_final: 0.7023 (tpp80) REVERT: A 477 TYR cc_start: 0.8540 (t80) cc_final: 0.7543 (t80) REVERT: B 315 ASP cc_start: 0.6559 (p0) cc_final: 0.6244 (p0) REVERT: B 402 MET cc_start: 0.7697 (tpp) cc_final: 0.7312 (tmm) REVERT: B 431 PHE cc_start: 0.8829 (t80) cc_final: 0.8628 (t80) REVERT: B 477 TYR cc_start: 0.8527 (t80) cc_final: 0.7612 (t80) outliers start: 9 outliers final: 7 residues processed: 123 average time/residue: 0.2065 time to fit residues: 33.2643 Evaluate side-chains 119 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 5 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108157 restraints weight = 9061.081| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.08 r_work: 0.3039 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2294 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= 0.173 Angle : 0.589 7.129 9530 Z= 0.291 Chirality : 0.040 0.166 1032 Planarity : 0.004 0.035 1166 Dihedral : 4.965 30.987 974 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.31), residues: 804 helix: 1.59 (0.22), residues: 620 sheet: None (None), residues: 0 loop : -2.76 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 429 HIS 0.003 0.001 HIS A 343 PHE 0.014 0.001 PHE A 389 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 434) hydrogen bonds : angle 4.57876 ( 1296) covalent geometry : bond 0.00413 ( 6998) covalent geometry : angle 0.58891 ( 9530) ********************** 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 115 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.783 Fit side-chains REVERT: A 67 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.7014 (mmm-85) REVERT: A 151 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8122 (mm-30) REVERT: A 315 ASP cc_start: 0.6680 (p0) cc_final: 0.6395 (p0) REVERT: A 389 PHE cc_start: 0.8897 (t80) cc_final: 0.8496 (t80) REVERT: A 402 MET cc_start: 0.7793 (tpp) cc_final: 0.7289 (tmm) REVERT: A 446 ARG cc_start: 0.7414 (ttt90) cc_final: 0.7077 (tpp80) REVERT: A 477 TYR cc_start: 0.8624 (t80) cc_final: 0.7666 (t80) REVERT: B 315 ASP cc_start: 0.6658 (p0) cc_final: 0.6371 (p0) REVERT: B 321 GLU cc_start: 0.7807 (pt0) cc_final: 0.7370 (pt0) REVERT: B 353 MET cc_start: 0.8746 (ptm) cc_final: 0.8307 (ptp) REVERT: B 389 PHE cc_start: 0.8957 (t80) cc_final: 0.8629 (t80) REVERT: B 402 MET cc_start: 0.7861 (tpp) cc_final: 0.7391 (tmm) REVERT: B 477 TYR cc_start: 0.8630 (t80) cc_final: 0.7749 (t80) outliers start: 8 outliers final: 7 residues processed: 114 average time/residue: 0.2135 time to fit residues: 31.8208 Evaluate side-chains 115 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.143830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111626 restraints weight = 8971.897| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.24 r_work: 0.3008 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6998 Z= 0.183 Angle : 0.604 7.156 9530 Z= 0.298 Chirality : 0.042 0.277 1032 Planarity : 0.004 0.035 1166 Dihedral : 5.091 31.942 974 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.12 % Allowed : 19.89 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.31), residues: 804 helix: 1.48 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -2.80 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 365 HIS 0.003 0.001 HIS A 343 PHE 0.011 0.001 PHE B 277 TYR 0.016 0.001 TYR B 417 ARG 0.004 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 434) hydrogen bonds : angle 4.65451 ( 1296) covalent geometry : bond 0.00439 ( 6998) covalent geometry : angle 0.60397 ( 9530) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.48 seconds wall clock time: 67 minutes 8.62 seconds (4028.62 seconds total)