Starting phenix.real_space_refine on Thu Jul 2 04:44:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etm_28594/07_2026/8etm_28594.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etm_28594/07_2026/8etm_28594.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/8etm_28594/07_2026/8etm_28594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etm_28594/07_2026/8etm_28594.map" model { file = "/net/cci-nas-00/data/ceres_data/8etm_28594/07_2026/8etm_28594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etm_28594/07_2026/8etm_28594.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 C 4524 2.51 5 N 1138 2.21 5 O 1090 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6800 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'WTT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'WTT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.17 Number of scatterers: 6800 At special positions: 0 Unit cell: (112.88, 98.77, 83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 F 6 9.00 O 1090 8.00 N 1138 7.00 C 4524 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 255.0 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 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 87 through 112 removed outlier: 5.575A pdb=" N ARG A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 131 through 157 removed outlier: 4.316A pdb=" N ASN A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 185 removed outlier: 3.541A pdb=" N GLY A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) 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: 3.578A pdb=" N ASN A 246 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 274 through 306 removed outlier: 4.439A pdb=" N VAL A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.622A pdb=" N ASP A 313 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.885A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.673A 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 370 through 375 removed outlier: 3.501A pdb=" N GLN A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 399 through 420 Processing helix chain 'A' and resid 421 through 424 Processing helix chain 'A' and resid 428 through 448 removed outlier: 4.435A 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: 4.297A pdb=" N VAL A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 112 removed outlier: 5.575A pdb=" N ARG B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 131 through 157 removed outlier: 4.315A pdb=" N ASN B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 185 removed outlier: 3.541A pdb=" N GLY B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) 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: 3.578A pdb=" N ASN B 246 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 274 through 306 removed outlier: 4.440A pdb=" N VAL B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 310 through 314 removed outlier: 3.622A pdb=" N ASP B 313 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.885A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.673A 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 370 through 375 removed outlier: 3.500A pdb=" N GLN B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 399 through 420 Processing helix chain 'B' and resid 421 through 424 Processing helix chain 'B' and resid 428 through 448 removed outlier: 4.434A 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: 4.297A pdb=" N VAL B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 470 " --> pdb=" O PRO B 466 " (cutoff:3.500A) 438 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: 0.63 Time building geometry restraints manager: 0.55 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: 1938 1.33 - 1.45: 1357 1.45 - 1.57: 3659 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 7022 Sorted by residual: bond pdb=" C WTT B 501 " pdb=" O WTT B 501 " ideal model delta sigma weight residual 1.251 1.310 -0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" C WTT A 501 " pdb=" O WTT A 501 " ideal model delta sigma weight residual 1.251 1.308 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C PHE A 342 " pdb=" N HIS A 343 " ideal model delta sigma weight residual 1.331 1.294 0.037 1.73e-02 3.34e+03 4.57e+00 bond pdb=" C PHE B 342 " pdb=" N HIS B 343 " ideal model delta sigma weight residual 1.331 1.294 0.037 1.73e-02 3.34e+03 4.57e+00 bond pdb=" C WTT A 501 " pdb=" O3 WTT A 501 " ideal model delta sigma weight residual 1.249 1.214 0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 7017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 9196 1.69 - 3.38: 268 3.38 - 5.07: 60 5.07 - 6.76: 29 6.76 - 8.44: 9 Bond angle restraints: 9562 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 113.18 121.08 -7.90 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY B 464 " pdb=" CA GLY B 464 " pdb=" C GLY B 464 " ideal model delta sigma weight residual 113.18 121.05 -7.87 2.37e+00 1.78e-01 1.10e+01 angle pdb=" C PHE B 342 " pdb=" N HIS B 343 " pdb=" CA HIS B 343 " ideal model delta sigma weight residual 122.42 116.69 5.73 1.77e+00 3.19e-01 1.05e+01 angle pdb=" C PHE A 342 " pdb=" N HIS A 343 " pdb=" CA HIS A 343 " ideal model delta sigma weight residual 122.42 116.70 5.72 1.77e+00 3.19e-01 1.04e+01 angle pdb=" C ILE B 379 " pdb=" CA ILE B 379 " pdb=" CB ILE B 379 " ideal model delta sigma weight residual 113.70 110.75 2.95 9.50e-01 1.11e+00 9.63e+00 ... (remaining 9557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 3827 24.57 - 49.13: 217 49.13 - 73.70: 15 73.70 - 98.26: 10 98.26 - 122.83: 1 Dihedral angle restraints: 4070 sinusoidal: 1658 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 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+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 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLY A 87 " pdb=" C GLY A 87 " pdb=" N ILE A 88 " pdb=" CA ILE A 88 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 4067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 1031 0.997 - 1.994: 0 1.994 - 2.991: 0 2.991 - 3.988: 0 3.988 - 4.985: 1 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C5 WTT A 501 " pdb=" C28 WTT A 501 " pdb=" C4 WTT A 501 " pdb=" C6 WTT A 501 " both_signs ideal model delta sigma weight residual False 2.50 -2.49 4.99 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C2 WTT B 501 " pdb=" C1 WTT B 501 " pdb=" C29 WTT B 501 " pdb=" C3 WTT B 501 " both_signs ideal model delta sigma weight residual False 2.42 2.60 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" C2 WTT A 501 " pdb=" C1 WTT A 501 " pdb=" C29 WTT A 501 " pdb=" C3 WTT A 501 " both_signs ideal model delta sigma weight residual False 2.42 2.58 -0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 1029 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 WTT B 501 " -0.090 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C14 WTT B 501 " 0.082 2.00e-02 2.50e+03 pdb=" C15 WTT B 501 " -0.350 2.00e-02 2.50e+03 pdb=" N1 WTT B 501 " 0.537 2.00e-02 2.50e+03 pdb=" O2 WTT B 501 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WTT B 501 " -0.019 2.00e-02 2.50e+03 1.54e-01 4.77e+02 pdb=" C11 WTT B 501 " 0.111 2.00e-02 2.50e+03 pdb=" C12 WTT B 501 " -0.135 2.00e-02 2.50e+03 pdb=" C13 WTT B 501 " -0.202 2.00e-02 2.50e+03 pdb=" C14 WTT B 501 " 0.297 2.00e-02 2.50e+03 pdb=" C23 WTT B 501 " -0.023 2.00e-02 2.50e+03 pdb=" C24 WTT B 501 " 0.109 2.00e-02 2.50e+03 pdb=" N2 WTT B 501 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 WTT A 501 " -0.161 2.00e-02 2.50e+03 1.86e-01 4.35e+02 pdb=" C14 WTT A 501 " 0.062 2.00e-02 2.50e+03 pdb=" C15 WTT A 501 " -0.223 2.00e-02 2.50e+03 pdb=" N1 WTT A 501 " 0.307 2.00e-02 2.50e+03 pdb=" O2 WTT A 501 " 0.016 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1491 2.76 - 3.30: 7068 3.30 - 3.83: 11384 3.83 - 4.37: 12824 4.37 - 4.90: 22328 Nonbonded interactions: 55095 Sorted by model distance: nonbonded pdb=" OE1 GLU A 351 " pdb=" NH2 ARG A 358 " model vdw 2.226 3.120 nonbonded pdb=" OE1 GLU B 351 " pdb=" NH2 ARG B 358 " model vdw 2.226 3.120 nonbonded pdb=" O TYR B 372 " pdb=" ND2 ASN B 376 " model vdw 2.249 3.120 nonbonded pdb=" O TYR A 372 " pdb=" ND2 ASN A 376 " model vdw 2.249 3.120 nonbonded pdb=" ND2 ASN B 378 " pdb=" O2 WTT B 501 " model vdw 2.252 3.120 ... (remaining 55090 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: 1.400 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.008 0.081 7023 Z= 0.374 Angle : 0.805 8.444 9562 Z= 0.414 Chirality : 0.162 4.985 1032 Planarity : 0.013 0.302 1170 Dihedral : 15.642 122.830 2506 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.24), residues: 804 helix: -1.46 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -4.91 (0.29), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 86 TYR 0.010 0.001 TYR A 417 PHE 0.017 0.002 PHE B 277 TRP 0.018 0.002 TRP A 377 HIS 0.005 0.001 HIS B 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.37 ( 7022) covalent geometry : angle 0.80464 / 0.41 ( 9562) hydrogen bonds : bond 0.11224 / 6.42 ( 438) hydrogen bonds : angle 6.42242 / 4.62 ( 1296) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** 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 149 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.168 Fit side-chains REVERT: A 131 TRP cc_start: 0.5126 (m-90) cc_final: 0.4061 (m100) REVERT: A 389 PHE cc_start: 0.7433 (t80) cc_final: 0.7163 (t80) REVERT: B 150 VAL cc_start: 0.7466 (t) cc_final: 0.7205 (t) REVERT: B 396 ARG cc_start: 0.3631 (ttm170) cc_final: 0.3220 (ttm170) REVERT: B 452 TYR cc_start: 0.7256 (m-80) cc_final: 0.6593 (m-80) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0862 time to fit residues: 16.1186 Evaluate side-chains 103 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 201 HIS A 306 ASN A 330 ASN A 451 ASN B 107 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 201 HIS B 306 ASN B 330 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136019 restraints weight = 9332.808| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.26 r_work: 0.3502 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7023 Z= 0.149 Angle : 0.738 13.186 9562 Z= 0.342 Chirality : 0.041 0.214 1032 Planarity : 0.005 0.039 1170 Dihedral : 7.307 52.268 962 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.68 % Allowed : 11.62 % Favored : 86.69 % 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: -1.10 (0.29), residues: 804 helix: 0.40 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -4.06 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 269 TYR 0.010 0.001 TYR B 372 PHE 0.019 0.002 PHE B 389 TRP 0.013 0.001 TRP B 334 HIS 0.003 0.001 HIS B 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 7022) covalent geometry : angle 0.73834 / 0.34 ( 9562) hydrogen bonds : bond 0.03952 / 2.64 ( 438) hydrogen bonds : angle 4.78056 / 3.44 ( 1296) Misc. bond : bond 0.00099 / 0.05 ( 1) *********************** 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 126 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.150 Fit side-chains REVERT: A 251 ASP cc_start: 0.6866 (t0) cc_final: 0.6662 (t0) REVERT: A 359 GLU cc_start: 0.7726 (tt0) cc_final: 0.7508 (tt0) REVERT: A 389 PHE cc_start: 0.8027 (t80) cc_final: 0.7580 (t80) REVERT: A 396 ARG cc_start: 0.4062 (ttm170) cc_final: 0.3451 (ttm170) REVERT: B 131 TRP cc_start: 0.5886 (m-90) cc_final: 0.4737 (m100) REVERT: B 150 VAL cc_start: 0.7357 (t) cc_final: 0.7109 (t) REVERT: B 359 GLU cc_start: 0.7638 (tt0) cc_final: 0.7437 (tt0) REVERT: B 396 ARG cc_start: 0.4620 (ttm170) cc_final: 0.4158 (ttm170) outliers start: 12 outliers final: 9 residues processed: 122 average time/residue: 0.0774 time to fit residues: 12.4153 Evaluate side-chains 105 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 63 optimal weight: 0.0870 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN A 292 GLN A 330 ASN A 366 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN B 366 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.127560 restraints weight = 9399.786| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.29 r_work: 0.3375 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7023 Z= 0.197 Angle : 0.755 12.827 9562 Z= 0.362 Chirality : 0.044 0.360 1032 Planarity : 0.005 0.054 1170 Dihedral : 6.885 48.797 962 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.94 % Allowed : 11.90 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.30), residues: 804 helix: 0.74 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -3.71 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.011 0.001 TYR A 339 PHE 0.013 0.002 PHE A 148 TRP 0.015 0.001 TRP B 377 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 7022) covalent geometry : angle 0.75520 / 0.36 ( 9562) hydrogen bonds : bond 0.04109 / 2.69 ( 438) hydrogen bonds : angle 4.89743 / 3.55 ( 1296) Misc. bond : bond 0.00095 / 0.05 ( 1) *********************** 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 160 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.232 Fit side-chains REVERT: A 119 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.5586 (tp-100) REVERT: A 250 ARG cc_start: 0.6118 (ttt90) cc_final: 0.5577 (tpt170) REVERT: A 298 GLN cc_start: 0.8188 (mt0) cc_final: 0.7794 (pt0) REVERT: A 396 ARG cc_start: 0.4762 (ttm170) cc_final: 0.4215 (ttm170) REVERT: A 425 MET cc_start: 0.8883 (mtt) cc_final: 0.8614 (mtt) REVERT: B 250 ARG cc_start: 0.6278 (ttt90) cc_final: 0.5756 (tpt170) REVERT: B 396 ARG cc_start: 0.5067 (ttm170) cc_final: 0.4643 (ttm170) outliers start: 21 outliers final: 14 residues processed: 158 average time/residue: 0.0780 time to fit residues: 15.9964 Evaluate side-chains 129 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 337 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN A 292 GLN A 354 GLN A 474 HIS ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 451 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128163 restraints weight = 9417.301| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.28 r_work: 0.3397 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7023 Z= 0.136 Angle : 0.684 11.591 9562 Z= 0.317 Chirality : 0.040 0.165 1032 Planarity : 0.004 0.039 1170 Dihedral : 6.413 48.620 962 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.08 % Allowed : 14.57 % Favored : 82.35 % 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: 0.06 (0.31), residues: 804 helix: 1.15 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.40 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.009 0.001 TYR B 339 PHE 0.012 0.001 PHE A 277 TRP 0.013 0.001 TRP B 377 HIS 0.002 0.000 HIS B 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 7022) covalent geometry : angle 0.68386 / 0.32 ( 9562) hydrogen bonds : bond 0.03700 / 2.45 ( 438) hydrogen bonds : angle 4.67490 / 3.37 ( 1296) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** 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 139 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.152 Fit side-chains REVERT: A 119 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.5841 (tp40) REVERT: A 250 ARG cc_start: 0.6290 (ttt90) cc_final: 0.5702 (tpt170) REVERT: A 269 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7756 (mmt-90) REVERT: A 275 LYS cc_start: 0.7721 (mppt) cc_final: 0.7283 (pttp) REVERT: A 359 GLU cc_start: 0.7881 (tt0) cc_final: 0.7609 (tp30) REVERT: A 396 ARG cc_start: 0.4856 (ttm170) cc_final: 0.4382 (ttm170) REVERT: B 143 PHE cc_start: 0.8681 (m-80) cc_final: 0.8395 (m-80) REVERT: B 250 ARG cc_start: 0.6318 (ttt90) cc_final: 0.5796 (tpt170) REVERT: B 275 LYS cc_start: 0.7681 (mppt) cc_final: 0.7177 (pttp) REVERT: B 359 GLU cc_start: 0.7879 (tt0) cc_final: 0.7619 (tp30) REVERT: B 396 ARG cc_start: 0.5047 (ttm170) cc_final: 0.4767 (ttm170) outliers start: 22 outliers final: 15 residues processed: 133 average time/residue: 0.0723 time to fit residues: 12.5001 Evaluate side-chains 124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127146 restraints weight = 9437.383| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.26 r_work: 0.3367 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7023 Z= 0.149 Angle : 0.705 13.022 9562 Z= 0.320 Chirality : 0.040 0.124 1032 Planarity : 0.004 0.037 1170 Dihedral : 6.124 52.397 962 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.50 % Allowed : 14.99 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.31), residues: 804 helix: 1.34 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -3.37 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.010 0.001 TYR B 339 PHE 0.011 0.001 PHE A 277 TRP 0.016 0.001 TRP B 131 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 7022) covalent geometry : angle 0.70455 / 0.32 ( 9562) hydrogen bonds : bond 0.03681 / 2.42 ( 438) hydrogen bonds : angle 4.67371 / 3.37 ( 1296) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** 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 136 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.156 Fit side-chains REVERT: A 250 ARG cc_start: 0.6424 (ttt90) cc_final: 0.5880 (tpt170) REVERT: A 269 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7832 (mmt-90) REVERT: A 275 LYS cc_start: 0.7813 (mppt) cc_final: 0.7338 (pttp) REVERT: A 290 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7625 (tt0) REVERT: A 353 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6841 (ptp) REVERT: A 359 GLU cc_start: 0.7942 (tt0) cc_final: 0.7662 (tp30) REVERT: A 396 ARG cc_start: 0.4978 (ttm170) cc_final: 0.4583 (ttm170) REVERT: B 143 PHE cc_start: 0.8778 (m-80) cc_final: 0.8445 (m-10) REVERT: B 250 ARG cc_start: 0.6394 (ttt90) cc_final: 0.5909 (tpt170) REVERT: B 275 LYS cc_start: 0.7727 (mppt) cc_final: 0.7211 (pttp) REVERT: B 353 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6311 (ppp) REVERT: B 359 GLU cc_start: 0.7899 (tt0) cc_final: 0.7636 (tp30) REVERT: B 396 ARG cc_start: 0.5138 (ttm170) cc_final: 0.4889 (ttm170) outliers start: 25 outliers final: 17 residues processed: 126 average time/residue: 0.0738 time to fit residues: 12.0893 Evaluate side-chains 124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.159079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127841 restraints weight = 9764.874| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.16 r_work: 0.3416 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7023 Z= 0.152 Angle : 0.706 14.589 9562 Z= 0.321 Chirality : 0.040 0.140 1032 Planarity : 0.005 0.039 1170 Dihedral : 6.030 56.366 962 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.52 % Allowed : 16.95 % Favored : 80.53 % 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: 0.53 (0.31), residues: 804 helix: 1.45 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.27 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.011 0.001 TYR B 339 PHE 0.010 0.001 PHE A 338 TRP 0.018 0.001 TRP B 131 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 7022) covalent geometry : angle 0.70633 / 0.32 ( 9562) hydrogen bonds : bond 0.03746 / 2.48 ( 438) hydrogen bonds : angle 4.66958 / 3.37 ( 1296) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** 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 132 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.149 Fit side-chains REVERT: A 250 ARG cc_start: 0.6591 (ttt90) cc_final: 0.6087 (tpt170) REVERT: A 275 LYS cc_start: 0.7867 (mppt) cc_final: 0.7475 (pttp) REVERT: A 290 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7743 (tt0) REVERT: A 292 GLN cc_start: 0.7920 (mt0) cc_final: 0.7711 (mt0) REVERT: A 353 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6809 (ptp) REVERT: A 359 GLU cc_start: 0.8059 (tt0) cc_final: 0.7834 (tp30) REVERT: A 389 PHE cc_start: 0.8316 (t80) cc_final: 0.8061 (t80) REVERT: A 396 ARG cc_start: 0.5188 (ttm170) cc_final: 0.4947 (ttm170) REVERT: B 143 PHE cc_start: 0.8820 (m-80) cc_final: 0.8552 (m-10) REVERT: B 250 ARG cc_start: 0.6608 (ttt90) cc_final: 0.6181 (tpt170) REVERT: B 275 LYS cc_start: 0.7927 (mppt) cc_final: 0.7476 (pttp) REVERT: B 353 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6448 (ppp) REVERT: B 359 GLU cc_start: 0.8076 (tt0) cc_final: 0.7846 (tp30) outliers start: 18 outliers final: 16 residues processed: 127 average time/residue: 0.0761 time to fit residues: 12.5524 Evaluate side-chains 115 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126044 restraints weight = 9626.014| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.03 r_work: 0.3435 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7023 Z= 0.133 Angle : 0.686 13.781 9562 Z= 0.310 Chirality : 0.039 0.156 1032 Planarity : 0.004 0.038 1170 Dihedral : 5.974 59.396 962 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.24 % Allowed : 18.49 % Favored : 79.27 % 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: 0.60 (0.31), residues: 804 helix: 1.50 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.25 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 219 TYR 0.010 0.001 TYR B 339 PHE 0.021 0.001 PHE A 413 TRP 0.017 0.001 TRP A 131 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7022) covalent geometry : angle 0.68640 / 0.31 ( 9562) hydrogen bonds : bond 0.03511 / 2.33 ( 438) hydrogen bonds : angle 4.63208 / 3.35 ( 1296) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** 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 122 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.252 Fit side-chains REVERT: A 106 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 250 ARG cc_start: 0.6453 (ttt90) cc_final: 0.6007 (tpt170) REVERT: A 275 LYS cc_start: 0.7893 (mppt) cc_final: 0.7526 (pttp) REVERT: A 290 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7743 (tt0) REVERT: A 292 GLN cc_start: 0.7939 (mt0) cc_final: 0.7713 (mt0) REVERT: A 353 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6759 (ptp) REVERT: A 359 GLU cc_start: 0.8034 (tt0) cc_final: 0.7834 (tp30) REVERT: B 250 ARG cc_start: 0.6627 (ttt90) cc_final: 0.6243 (tpt170) REVERT: B 275 LYS cc_start: 0.7907 (mppt) cc_final: 0.7512 (pttp) REVERT: B 284 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 324 LEU cc_start: 0.7281 (mm) cc_final: 0.7074 (mp) REVERT: B 353 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6391 (ppp) REVERT: B 359 GLU cc_start: 0.8045 (tt0) cc_final: 0.7844 (tp30) outliers start: 16 outliers final: 12 residues processed: 117 average time/residue: 0.1026 time to fit residues: 15.3392 Evaluate side-chains 117 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.154148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124226 restraints weight = 9853.971| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.04 r_work: 0.3385 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7023 Z= 0.151 Angle : 0.691 13.613 9562 Z= 0.314 Chirality : 0.040 0.176 1032 Planarity : 0.004 0.037 1170 Dihedral : 6.068 58.398 962 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.52 % Allowed : 18.49 % 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 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: 0.56 (0.31), residues: 804 helix: 1.48 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.30 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 220 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE B 277 TRP 0.018 0.001 TRP A 131 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7022) covalent geometry : angle 0.69053 / 0.31 ( 9562) hydrogen bonds : bond 0.03682 / 2.42 ( 438) hydrogen bonds : angle 4.64824 / 3.37 ( 1296) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** 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 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.236 Fit side-chains REVERT: A 250 ARG cc_start: 0.6571 (ttt90) cc_final: 0.6070 (tpt170) REVERT: A 275 LYS cc_start: 0.7893 (mppt) cc_final: 0.7502 (pttp) REVERT: A 290 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7772 (tt0) REVERT: A 292 GLN cc_start: 0.7941 (mt0) cc_final: 0.7687 (mt0) REVERT: A 353 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6859 (ptp) REVERT: A 359 GLU cc_start: 0.8198 (tt0) cc_final: 0.7943 (tp30) REVERT: B 250 ARG cc_start: 0.6635 (ttt90) cc_final: 0.6150 (tpt170) REVERT: B 275 LYS cc_start: 0.7980 (mppt) cc_final: 0.7517 (pttp) REVERT: B 292 GLN cc_start: 0.7890 (mt0) cc_final: 0.7643 (mt0) REVERT: B 353 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.6576 (ppp) REVERT: B 359 GLU cc_start: 0.8104 (tt0) cc_final: 0.7882 (tp30) REVERT: B 434 MET cc_start: 0.7936 (tpt) cc_final: 0.7431 (tpt) outliers start: 18 outliers final: 16 residues processed: 124 average time/residue: 0.0946 time to fit residues: 15.1379 Evaluate side-chains 124 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 451 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124838 restraints weight = 9843.421| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.04 r_work: 0.3377 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7023 Z= 0.162 Angle : 0.705 13.837 9562 Z= 0.323 Chirality : 0.041 0.177 1032 Planarity : 0.005 0.040 1170 Dihedral : 6.085 57.711 962 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.66 % Allowed : 18.49 % Favored : 78.85 % 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: 0.47 (0.31), residues: 804 helix: 1.43 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.40 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 220 TYR 0.011 0.001 TYR B 339 PHE 0.011 0.001 PHE A 338 TRP 0.025 0.001 TRP A 131 HIS 0.002 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 7022) covalent geometry : angle 0.70539 / 0.32 ( 9562) hydrogen bonds : bond 0.03731 / 2.45 ( 438) hydrogen bonds : angle 4.67616 / 3.40 ( 1296) Misc. bond : bond 0.00044 / 0.02 ( 1) *********************** 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 129 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.199 Fit side-chains REVERT: A 250 ARG cc_start: 0.6684 (ttt90) cc_final: 0.6205 (tpt170) REVERT: A 275 LYS cc_start: 0.7928 (mppt) cc_final: 0.7527 (pttp) REVERT: A 290 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7746 (tt0) REVERT: A 292 GLN cc_start: 0.7952 (mt0) cc_final: 0.7686 (mt0) REVERT: A 353 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.6895 (ptp) REVERT: A 434 MET cc_start: 0.8063 (tpt) cc_final: 0.7574 (tpt) REVERT: B 250 ARG cc_start: 0.6701 (ttt90) cc_final: 0.6257 (tpt170) REVERT: B 275 LYS cc_start: 0.7952 (mppt) cc_final: 0.7471 (pttp) REVERT: B 292 GLN cc_start: 0.7896 (mt0) cc_final: 0.7647 (mt0) REVERT: B 353 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.6643 (ppp) REVERT: B 359 GLU cc_start: 0.8221 (tt0) cc_final: 0.7976 (tp30) REVERT: B 434 MET cc_start: 0.8002 (tpt) cc_final: 0.7560 (tpt) outliers start: 19 outliers final: 16 residues processed: 123 average time/residue: 0.0995 time to fit residues: 15.5856 Evaluate side-chains 128 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.126764 restraints weight = 9652.611| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.03 r_work: 0.3420 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.6955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7023 Z= 0.120 Angle : 0.678 13.880 9562 Z= 0.309 Chirality : 0.039 0.174 1032 Planarity : 0.004 0.037 1170 Dihedral : 5.788 59.276 962 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.82 % Allowed : 19.47 % Favored : 78.71 % 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: 0.63 (0.31), residues: 804 helix: 1.60 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.52 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 220 TYR 0.009 0.001 TYR B 339 PHE 0.010 0.001 PHE A 277 TRP 0.020 0.001 TRP A 131 HIS 0.002 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7022) covalent geometry : angle 0.67795 / 0.31 ( 9562) hydrogen bonds : bond 0.03413 / 2.25 ( 438) hydrogen bonds : angle 4.57482 / 3.33 ( 1296) Misc. bond : bond 0.00029 / 0.02 ( 1) ********************** 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 130 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.312 Fit side-chains REVERT: A 161 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6863 (mt-10) REVERT: A 250 ARG cc_start: 0.6546 (ttt90) cc_final: 0.6094 (tpt170) REVERT: A 275 LYS cc_start: 0.7862 (mppt) cc_final: 0.7500 (pttp) REVERT: A 290 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7716 (tt0) REVERT: A 292 GLN cc_start: 0.7868 (mt0) cc_final: 0.7580 (mt0) REVERT: A 353 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6018 (ppp) REVERT: A 434 MET cc_start: 0.8075 (tpt) cc_final: 0.7555 (tpt) REVERT: B 250 ARG cc_start: 0.6633 (ttt90) cc_final: 0.6194 (tpt170) REVERT: B 275 LYS cc_start: 0.7974 (mppt) cc_final: 0.7489 (pttp) REVERT: B 292 GLN cc_start: 0.7828 (mt0) cc_final: 0.7559 (mt0) REVERT: B 353 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6466 (ppp) REVERT: B 389 PHE cc_start: 0.8297 (t80) cc_final: 0.8036 (t80) REVERT: B 434 MET cc_start: 0.7956 (tpt) cc_final: 0.7475 (tpt) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.1055 time to fit residues: 16.8692 Evaluate side-chains 121 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 337 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 337 PHE Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 383 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126171 restraints weight = 9530.574| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.18 r_work: 0.3380 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7023 Z= 0.118 Angle : 0.673 13.599 9562 Z= 0.306 Chirality : 0.039 0.167 1032 Planarity : 0.004 0.036 1170 Dihedral : 5.637 57.002 962 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.96 % Allowed : 19.47 % Favored : 78.57 % 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: 0.68 (0.31), residues: 804 helix: 1.63 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -3.52 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 220 TYR 0.010 0.001 TYR A 339 PHE 0.011 0.001 PHE A 389 TRP 0.024 0.001 TRP A 131 HIS 0.001 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7022) covalent geometry : angle 0.67279 / 0.31 ( 9562) hydrogen bonds : bond 0.03357 / 2.22 ( 438) hydrogen bonds : angle 4.55111 / 3.31 ( 1296) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.15 seconds wall clock time: 24 minutes 42.92 seconds (1482.92 seconds total)