Starting phenix.real_space_refine on Thu Jul 2 08:22:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.cif" model { file = "/net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f40_31443/07_2026/7f40_31443.map" } resolution = 3.49 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= 0.006 sd= 0.068 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 P 8 5.49 5 S 48 5.16 5 C 5098 2.51 5 N 1162 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7596 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 430} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'3IX': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 2.77, per 1000 atoms: 0.36 Number of scatterers: 7596 At special positions: 0 Unit cell: (112.66, 117.82, 75.68, 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 48 16.00 P 8 15.00 O 1280 8.00 N 1162 7.00 C 5098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 408.9 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 68.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.661A pdb=" N GLU A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.606A pdb=" N LEU A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.158A pdb=" N PHE A 68 " --> pdb=" O MET A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 100 removed outlier: 4.136A pdb=" N ILE A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.194A pdb=" N SER A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 147 removed outlier: 3.896A pdb=" N VAL A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 177 removed outlier: 3.670A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 removed outlier: 3.625A pdb=" N GLY A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.638A pdb=" N LYS A 227 " --> pdb=" O GLN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 262 Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 293 through 313 removed outlier: 3.907A pdb=" N LYS A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.655A pdb=" N THR A 340 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 4.196A pdb=" N ILE A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 344 through 349' Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.617A pdb=" N ASN A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 388 removed outlier: 4.028A pdb=" N HIS A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 415 Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.729A pdb=" N LEU A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 455 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 457 through 467 removed outlier: 4.236A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 Proline residue: A 484 - end of helix Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.661A pdb=" N GLU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.606A pdb=" N LEU B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 75 removed outlier: 4.158A pdb=" N PHE B 68 " --> pdb=" O MET B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 100 removed outlier: 4.136A pdb=" N ILE B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.195A pdb=" N SER B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 147 removed outlier: 3.897A pdb=" N VAL B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 177 removed outlier: 3.670A pdb=" N GLY B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 removed outlier: 3.625A pdb=" N GLY B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.638A pdb=" N LYS B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 262 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 293 through 313 removed outlier: 3.907A pdb=" N LYS B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.653A pdb=" N THR B 340 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.617A pdb=" N ASN B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 388 removed outlier: 4.028A pdb=" N HIS B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 415 Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.728A pdb=" N LEU B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 457 through 467 removed outlier: 4.236A pdb=" N SER B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 490 Proline residue: B 484 - end of helix 389 hydrogen bonds defined for protein. 1143 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: 0.77 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1080 1.30 - 1.43: 2375 1.43 - 1.57: 4273 1.57 - 1.70: 16 1.70 - 1.83: 80 Bond restraints: 7824 Sorted by residual: bond pdb=" C48 3IX B 601 " pdb=" C49 3IX B 601 " ideal model delta sigma weight residual 1.533 1.292 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C48 3IX A 601 " pdb=" C49 3IX A 601 " ideal model delta sigma weight residual 1.533 1.293 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C48 3IX A 601 " pdb=" O52 3IX A 601 " ideal model delta sigma weight residual 1.428 1.616 -0.188 2.00e-02 2.50e+03 8.85e+01 bond pdb=" C48 3IX B 601 " pdb=" O52 3IX B 601 " ideal model delta sigma weight residual 1.428 1.616 -0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C49 3IX B 601 " pdb=" O64 3IX B 601 " ideal model delta sigma weight residual 1.389 1.521 -0.132 2.00e-02 2.50e+03 4.36e+01 ... (remaining 7819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 10497 4.96 - 9.93: 85 9.93 - 14.89: 32 14.89 - 19.86: 4 19.86 - 24.82: 4 Bond angle restraints: 10622 Sorted by residual: angle pdb=" C19 PCW A 602 " pdb=" C20 PCW A 602 " pdb=" C21 PCW A 602 " ideal model delta sigma weight residual 127.82 152.64 -24.82 3.00e+00 1.11e-01 6.85e+01 angle pdb=" C19 PCW B 602 " pdb=" C20 PCW B 602 " pdb=" C21 PCW B 602 " ideal model delta sigma weight residual 127.82 152.63 -24.81 3.00e+00 1.11e-01 6.84e+01 angle pdb=" C15 PCW A 602 " pdb=" C16 PCW A 602 " pdb=" C17 PCW A 602 " ideal model delta sigma weight residual 112.46 135.74 -23.28 3.00e+00 1.11e-01 6.02e+01 angle pdb=" C15 PCW B 602 " pdb=" C16 PCW B 602 " pdb=" C17 PCW B 602 " ideal model delta sigma weight residual 112.46 135.73 -23.27 3.00e+00 1.11e-01 6.02e+01 angle pdb=" C06 3IX A 601 " pdb=" C07 3IX A 601 " pdb=" C08 3IX A 601 " ideal model delta sigma weight residual 127.11 108.48 18.63 3.00e+00 1.11e-01 3.86e+01 ... (remaining 10617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.23: 4254 29.23 - 58.46: 264 58.46 - 87.69: 38 87.69 - 116.91: 0 116.91 - 146.14: 2 Dihedral angle restraints: 4558 sinusoidal: 1922 harmonic: 2636 Sorted by residual: dihedral pdb=" N PCW B 602 " pdb=" C4 PCW B 602 " pdb=" C5 PCW B 602 " pdb=" O4P PCW B 602 " ideal model delta sinusoidal sigma weight residual -66.66 79.48 -146.14 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" N PCW A 602 " pdb=" C4 PCW A 602 " pdb=" C5 PCW A 602 " pdb=" O4P PCW A 602 " ideal model delta sinusoidal sigma weight residual -66.66 79.47 -146.13 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA VAL A 233 " pdb=" C VAL A 233 " pdb=" N PRO A 234 " pdb=" CA PRO A 234 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1004 0.061 - 0.123: 148 0.123 - 0.184: 8 0.184 - 0.246: 2 0.246 - 0.307: 2 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C33 3IX B 601 " pdb=" C31 3IX B 601 " pdb=" C34 3IX B 601 " pdb=" O69 3IX B 601 " both_signs ideal model delta sigma weight residual False -2.20 -2.50 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C33 3IX A 601 " pdb=" C31 3IX A 601 " pdb=" C34 3IX A 601 " pdb=" O69 3IX A 601 " both_signs ideal model delta sigma weight residual False -2.20 -2.50 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2 PCW A 602 " pdb=" C1 PCW A 602 " pdb=" C3 PCW A 602 " pdb=" O2 PCW A 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1161 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 179 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 180 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 179 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 180 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 234 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.025 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2204 2.81 - 3.34: 7440 3.34 - 3.86: 11760 3.86 - 4.38: 12378 4.38 - 4.90: 21774 Nonbonded interactions: 55556 Sorted by model distance: nonbonded pdb=" OG SER A 107 " pdb=" OH TYR A 206 " model vdw 2.293 3.040 nonbonded pdb=" OG SER B 107 " pdb=" OH TYR B 206 " model vdw 2.293 3.040 nonbonded pdb=" N25 3IX A 601 " pdb=" S22 3IX A 601 " model vdw 2.307 2.784 nonbonded pdb=" N25 3IX B 601 " pdb=" S22 3IX B 601 " model vdw 2.307 2.784 nonbonded pdb=" NH1 ARG A 283 " pdb=" OG SER A 467 " model vdw 2.310 3.120 ... (remaining 55551 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 0.241 7824 Z= 0.430 Angle : 1.265 24.824 10622 Z= 0.495 Chirality : 0.044 0.307 1164 Planarity : 0.005 0.067 1272 Dihedral : 18.267 146.142 2878 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.42 (0.29), residues: 894 helix: 1.11 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.73 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.017 0.001 TYR B 143 PHE 0.018 0.001 PHE B 115 TRP 0.010 0.001 TRP B 290 HIS 0.002 0.001 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00875 / 0.43 ( 7824) covalent geometry : angle 1.26537 / 0.50 (10622) hydrogen bonds : bond 0.13968 / 9.74 ( 389) hydrogen bonds : angle 4.81855 / 3.55 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 416 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6540 (ptt90) REVERT: B 416 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6746 (mtt90) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0488 time to fit residues: 10.7306 Evaluate side-chains 132 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.172329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131520 restraints weight = 10942.887| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.98 r_work: 0.3385 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7824 Z= 0.150 Angle : 0.647 6.736 10622 Z= 0.322 Chirality : 0.041 0.168 1164 Planarity : 0.005 0.044 1272 Dihedral : 15.260 121.457 1214 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.89 % Allowed : 11.36 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.34 (0.29), residues: 894 helix: 1.10 (0.22), residues: 578 sheet: None (None), residues: 0 loop : -2.88 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.019 0.001 TYR B 269 PHE 0.008 0.001 PHE B 204 TRP 0.011 0.001 TRP A 461 HIS 0.003 0.002 HIS B 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 7824) covalent geometry : angle 0.64679 / 0.32 (10622) hydrogen bonds : bond 0.05038 / 3.33 ( 389) hydrogen bonds : angle 3.80434 / 2.80 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.227 Fit side-chains REVERT: A 219 MET cc_start: 0.8465 (tpt) cc_final: 0.7803 (tpp) REVERT: A 416 ARG cc_start: 0.7261 (mtt180) cc_final: 0.6235 (ptt90) REVERT: A 463 LYS cc_start: 0.7969 (tmmt) cc_final: 0.7478 (tmmt) REVERT: B 188 ARG cc_start: 0.8171 (mpp80) cc_final: 0.7955 (mpp80) REVERT: B 337 LEU cc_start: 0.8968 (tp) cc_final: 0.8708 (tt) REVERT: B 416 ARG cc_start: 0.7322 (mtt180) cc_final: 0.6281 (ptt90) outliers start: 15 outliers final: 11 residues processed: 157 average time/residue: 0.0644 time to fit residues: 14.1178 Evaluate side-chains 153 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.168103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.126628 restraints weight = 10805.611| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.97 r_work: 0.3347 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7824 Z= 0.162 Angle : 0.636 7.094 10622 Z= 0.320 Chirality : 0.041 0.167 1164 Planarity : 0.004 0.047 1272 Dihedral : 14.253 119.455 1214 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.41 % Allowed : 17.30 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.23 (0.29), residues: 894 helix: 1.18 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -2.85 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.019 0.001 TYR A 465 PHE 0.010 0.001 PHE B 364 TRP 0.014 0.001 TRP A 461 HIS 0.004 0.002 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 7824) covalent geometry : angle 0.63597 / 0.32 (10622) hydrogen bonds : bond 0.05336 / 3.54 ( 389) hydrogen bonds : angle 3.69109 / 2.72 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.171 Fit side-chains REVERT: A 400 MET cc_start: 0.7808 (tpp) cc_final: 0.7139 (tpp) REVERT: A 401 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8665 (tm-30) REVERT: A 404 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 416 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6324 (ptt90) REVERT: A 417 ASP cc_start: 0.8890 (t0) cc_final: 0.8615 (t0) REVERT: A 463 LYS cc_start: 0.8048 (tmmt) cc_final: 0.7518 (tmmt) REVERT: B 219 MET cc_start: 0.8369 (tpp) cc_final: 0.8044 (tpp) REVERT: B 416 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6319 (ptt90) outliers start: 27 outliers final: 23 residues processed: 163 average time/residue: 0.0586 time to fit residues: 13.8491 Evaluate side-chains 173 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 486 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 72 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.172050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130995 restraints weight = 10950.804| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.00 r_work: 0.3414 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7824 Z= 0.124 Angle : 0.595 7.684 10622 Z= 0.299 Chirality : 0.040 0.181 1164 Planarity : 0.004 0.045 1272 Dihedral : 13.266 121.197 1214 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.91 % Allowed : 19.95 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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 (0.30), residues: 894 helix: 1.44 (0.23), residues: 580 sheet: None (None), residues: 0 loop : -2.80 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 188 TYR 0.015 0.001 TYR A 465 PHE 0.010 0.001 PHE A 476 TRP 0.009 0.001 TRP A 461 HIS 0.003 0.001 HIS A 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7824) covalent geometry : angle 0.59545 / 0.30 (10622) hydrogen bonds : bond 0.04129 / 2.71 ( 389) hydrogen bonds : angle 3.48988 / 2.56 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.207 Fit side-chains REVERT: A 219 MET cc_start: 0.8369 (tpp) cc_final: 0.8050 (tpp) REVERT: A 250 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7203 (mp) REVERT: A 367 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7635 (tt) REVERT: A 400 MET cc_start: 0.7760 (tpp) cc_final: 0.7053 (tpp) REVERT: A 401 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 404 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 416 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6249 (ptt90) REVERT: A 417 ASP cc_start: 0.8942 (t0) cc_final: 0.8620 (t0) REVERT: A 463 LYS cc_start: 0.8094 (tmmt) cc_final: 0.7631 (tmmt) REVERT: B 219 MET cc_start: 0.8272 (tpp) cc_final: 0.7937 (tpp) REVERT: B 250 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7081 (mp) REVERT: B 367 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7629 (tt) REVERT: B 416 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6298 (ptt90) REVERT: B 417 ASP cc_start: 0.8836 (t0) cc_final: 0.8566 (t0) outliers start: 31 outliers final: 17 residues processed: 175 average time/residue: 0.0520 time to fit residues: 13.3235 Evaluate side-chains 177 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 59 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.175206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135520 restraints weight = 10854.905| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.90 r_work: 0.3477 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 7824 Z= 0.113 Angle : 0.580 8.314 10622 Z= 0.285 Chirality : 0.039 0.178 1164 Planarity : 0.004 0.045 1272 Dihedral : 12.350 121.722 1214 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.54 % Allowed : 21.34 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.23 (0.30), residues: 894 helix: 1.60 (0.23), residues: 580 sheet: None (None), residues: 0 loop : -2.80 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 188 TYR 0.014 0.001 TYR A 269 PHE 0.011 0.001 PHE A 476 TRP 0.008 0.001 TRP B 461 HIS 0.002 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7824) covalent geometry : angle 0.57968 / 0.29 (10622) hydrogen bonds : bond 0.03548 / 2.34 ( 389) hydrogen bonds : angle 3.38135 / 2.47 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.167 Fit side-chains REVERT: A 219 MET cc_start: 0.8323 (tpp) cc_final: 0.7933 (tpp) REVERT: A 250 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7208 (mp) REVERT: A 269 TYR cc_start: 0.7635 (t80) cc_final: 0.7276 (t80) REVERT: A 367 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7601 (tt) REVERT: A 400 MET cc_start: 0.7633 (tpp) cc_final: 0.6906 (tpp) REVERT: A 401 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 404 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7899 (mp) REVERT: A 416 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6282 (ptt90) REVERT: A 417 ASP cc_start: 0.8928 (t0) cc_final: 0.8590 (t0) REVERT: A 463 LYS cc_start: 0.8077 (tmmt) cc_final: 0.7689 (tmmt) REVERT: B 188 ARG cc_start: 0.7992 (mpp80) cc_final: 0.7610 (mpp80) REVERT: B 219 MET cc_start: 0.8239 (tpp) cc_final: 0.7898 (tpp) REVERT: B 250 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7146 (mp) REVERT: B 269 TYR cc_start: 0.7667 (t80) cc_final: 0.7302 (t80) REVERT: B 344 PHE cc_start: 0.7644 (m-80) cc_final: 0.7138 (t80) REVERT: B 367 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (tt) REVERT: B 416 ARG cc_start: 0.7255 (mtt180) cc_final: 0.6298 (ptt90) REVERT: B 417 ASP cc_start: 0.8939 (t0) cc_final: 0.8614 (t0) REVERT: B 479 LEU cc_start: 0.7452 (tt) cc_final: 0.7200 (tt) outliers start: 28 outliers final: 15 residues processed: 162 average time/residue: 0.0507 time to fit residues: 12.0306 Evaluate side-chains 165 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 overall best weight: 0.4334 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.175912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136166 restraints weight = 10548.589| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.83 r_work: 0.3478 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7824 Z= 0.108 Angle : 0.569 8.414 10622 Z= 0.279 Chirality : 0.038 0.165 1164 Planarity : 0.005 0.066 1272 Dihedral : 11.989 121.739 1214 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.91 % Allowed : 22.10 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 894 helix: 1.67 (0.23), residues: 580 sheet: None (None), residues: 0 loop : -2.81 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.014 0.001 TYR A 82 PHE 0.011 0.001 PHE B 476 TRP 0.014 0.001 TRP A 458 HIS 0.003 0.001 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 7824) covalent geometry : angle 0.56917 / 0.28 (10622) hydrogen bonds : bond 0.03428 / 2.26 ( 389) hydrogen bonds : angle 3.33147 / 2.43 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.218 Fit side-chains REVERT: A 219 MET cc_start: 0.8326 (tpp) cc_final: 0.7982 (tpp) REVERT: A 250 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7214 (mp) REVERT: A 269 TYR cc_start: 0.7632 (t80) cc_final: 0.7261 (t80) REVERT: A 306 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: A 367 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 400 MET cc_start: 0.7691 (tpp) cc_final: 0.6990 (tpp) REVERT: A 401 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8564 (tm-30) REVERT: A 404 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7888 (mp) REVERT: A 416 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6300 (ptt90) REVERT: A 417 ASP cc_start: 0.8891 (t0) cc_final: 0.8555 (t0) REVERT: A 463 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7648 (tmmt) REVERT: B 219 MET cc_start: 0.8237 (tpp) cc_final: 0.7936 (tpp) REVERT: B 250 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7170 (mp) REVERT: B 269 TYR cc_start: 0.7648 (t80) cc_final: 0.7326 (t80) REVERT: B 306 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: B 367 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7526 (tt) REVERT: B 401 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 416 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6254 (ptt90) REVERT: B 417 ASP cc_start: 0.8964 (t0) cc_final: 0.8623 (t0) outliers start: 31 outliers final: 15 residues processed: 158 average time/residue: 0.0549 time to fit residues: 12.6074 Evaluate side-chains 166 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.172576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131742 restraints weight = 10801.215| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.97 r_work: 0.3440 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7824 Z= 0.124 Angle : 0.592 8.593 10622 Z= 0.289 Chirality : 0.039 0.160 1164 Planarity : 0.005 0.068 1272 Dihedral : 11.808 121.079 1214 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.41 % Allowed : 23.61 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.25 (0.30), residues: 894 helix: 1.62 (0.23), residues: 580 sheet: None (None), residues: 0 loop : -2.82 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.016 0.001 TYR A 465 PHE 0.013 0.001 PHE B 476 TRP 0.014 0.001 TRP B 461 HIS 0.003 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7824) covalent geometry : angle 0.59205 / 0.29 (10622) hydrogen bonds : bond 0.04011 / 2.63 ( 389) hydrogen bonds : angle 3.36836 / 2.46 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.180 Fit side-chains REVERT: A 219 MET cc_start: 0.8309 (tpp) cc_final: 0.7967 (tpp) REVERT: A 250 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7205 (mp) REVERT: A 306 GLU cc_start: 0.7822 (tp30) cc_final: 0.7566 (tt0) REVERT: A 367 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7569 (tt) REVERT: A 400 MET cc_start: 0.7797 (tpp) cc_final: 0.7062 (tpp) REVERT: A 404 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 416 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6262 (ptt90) REVERT: A 417 ASP cc_start: 0.8914 (t0) cc_final: 0.8582 (t0) REVERT: A 463 LYS cc_start: 0.8030 (tmmt) cc_final: 0.7626 (tmmt) REVERT: B 188 ARG cc_start: 0.8131 (mpp80) cc_final: 0.7609 (mpp80) REVERT: B 219 MET cc_start: 0.8233 (tpp) cc_final: 0.7944 (tpp) REVERT: B 250 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7176 (mp) REVERT: B 306 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: B 344 PHE cc_start: 0.7710 (m-80) cc_final: 0.7138 (t80) REVERT: B 367 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7504 (tt) REVERT: B 401 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8641 (tm-30) REVERT: B 416 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6252 (ptt90) REVERT: B 417 ASP cc_start: 0.8950 (t0) cc_final: 0.8584 (t0) outliers start: 27 outliers final: 17 residues processed: 156 average time/residue: 0.0564 time to fit residues: 12.7817 Evaluate side-chains 166 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.132267 restraints weight = 10915.680| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.99 r_work: 0.3434 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7824 Z= 0.119 Angle : 0.594 8.674 10622 Z= 0.291 Chirality : 0.039 0.178 1164 Planarity : 0.005 0.070 1272 Dihedral : 11.593 121.304 1214 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.28 % Allowed : 25.38 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.26 (0.30), residues: 894 helix: 1.63 (0.23), residues: 580 sheet: None (None), residues: 0 loop : -2.83 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 188 TYR 0.015 0.001 TYR B 465 PHE 0.014 0.001 PHE B 476 TRP 0.014 0.001 TRP A 461 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 7824) covalent geometry : angle 0.59436 / 0.29 (10622) hydrogen bonds : bond 0.03928 / 2.57 ( 389) hydrogen bonds : angle 3.35306 / 2.45 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.274 Fit side-chains REVERT: A 219 MET cc_start: 0.8306 (tpp) cc_final: 0.7965 (tpp) REVERT: A 250 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7255 (mp) REVERT: A 306 GLU cc_start: 0.7806 (tp30) cc_final: 0.7520 (tt0) REVERT: A 400 MET cc_start: 0.7799 (tpp) cc_final: 0.7035 (tpp) REVERT: A 401 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 404 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 416 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6310 (ptt90) REVERT: A 417 ASP cc_start: 0.8917 (t0) cc_final: 0.8612 (t0) REVERT: A 463 LYS cc_start: 0.8091 (tmmt) cc_final: 0.7671 (tmmt) REVERT: B 219 MET cc_start: 0.8236 (tpp) cc_final: 0.7906 (tpp) REVERT: B 250 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7223 (mp) REVERT: B 306 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: B 344 PHE cc_start: 0.7713 (m-80) cc_final: 0.7144 (t80) REVERT: B 401 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8634 (tm-30) REVERT: B 416 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6291 (ptt90) REVERT: B 417 ASP cc_start: 0.8957 (t0) cc_final: 0.8623 (t0) outliers start: 26 outliers final: 17 residues processed: 161 average time/residue: 0.0548 time to fit residues: 12.7641 Evaluate side-chains 166 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.171093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129896 restraints weight = 10789.079| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.00 r_work: 0.3405 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7824 Z= 0.134 Angle : 0.617 8.757 10622 Z= 0.304 Chirality : 0.040 0.174 1164 Planarity : 0.005 0.072 1272 Dihedral : 11.562 120.664 1214 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.16 % Allowed : 24.37 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.19 (0.30), residues: 894 helix: 1.58 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -2.83 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 188 TYR 0.019 0.001 TYR A 465 PHE 0.013 0.001 PHE B 476 TRP 0.019 0.001 TRP A 461 HIS 0.004 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 7824) covalent geometry : angle 0.61659 / 0.30 (10622) hydrogen bonds : bond 0.04215 / 2.77 ( 389) hydrogen bonds : angle 3.44377 / 2.52 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.286 Fit side-chains REVERT: A 219 MET cc_start: 0.8292 (tpp) cc_final: 0.7964 (tpp) REVERT: A 250 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7201 (mp) REVERT: A 306 GLU cc_start: 0.7777 (tp30) cc_final: 0.7493 (tt0) REVERT: A 367 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7548 (tt) REVERT: A 400 MET cc_start: 0.7791 (tpp) cc_final: 0.6984 (tpp) REVERT: A 401 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8563 (tm-30) REVERT: A 404 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7910 (mp) REVERT: A 416 ARG cc_start: 0.7252 (mtt180) cc_final: 0.6025 (ttp-170) REVERT: A 417 ASP cc_start: 0.8951 (t0) cc_final: 0.8644 (t0) REVERT: A 463 LYS cc_start: 0.7986 (tmmt) cc_final: 0.7574 (tmmt) REVERT: B 219 MET cc_start: 0.8214 (tpp) cc_final: 0.7911 (tpp) REVERT: B 250 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7160 (mp) REVERT: B 344 PHE cc_start: 0.7735 (m-80) cc_final: 0.7149 (t80) REVERT: B 367 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7545 (tt) REVERT: B 401 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8647 (tm-30) REVERT: B 416 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6216 (ptt90) REVERT: B 417 ASP cc_start: 0.8999 (t0) cc_final: 0.8660 (t0) REVERT: B 479 LEU cc_start: 0.7477 (tt) cc_final: 0.7247 (tt) outliers start: 25 outliers final: 18 residues processed: 158 average time/residue: 0.0613 time to fit residues: 13.9679 Evaluate side-chains 167 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 67 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.171817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131447 restraints weight = 10786.261| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.91 r_work: 0.3424 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 7824 Z= 0.127 Angle : 0.620 8.798 10622 Z= 0.306 Chirality : 0.039 0.166 1164 Planarity : 0.005 0.074 1272 Dihedral : 11.444 120.899 1214 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.90 % Allowed : 24.49 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.25 (0.30), residues: 894 helix: 1.61 (0.22), residues: 578 sheet: None (None), residues: 0 loop : -2.76 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.017 0.001 TYR A 465 PHE 0.011 0.001 PHE A 476 TRP 0.021 0.001 TRP A 461 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7824) covalent geometry : angle 0.62017 / 0.31 (10622) hydrogen bonds : bond 0.04041 / 2.66 ( 389) hydrogen bonds : angle 3.44289 / 2.53 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.282 Fit side-chains REVERT: A 219 MET cc_start: 0.8306 (tpp) cc_final: 0.7963 (tpp) REVERT: A 250 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7257 (mp) REVERT: A 306 GLU cc_start: 0.7773 (tp30) cc_final: 0.7492 (tt0) REVERT: A 367 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7595 (tt) REVERT: A 400 MET cc_start: 0.7789 (tpp) cc_final: 0.6981 (tpp) REVERT: A 401 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 404 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7944 (mp) REVERT: A 416 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6290 (ptt90) REVERT: A 417 ASP cc_start: 0.8932 (t0) cc_final: 0.8677 (t0) REVERT: A 463 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7588 (tmmt) REVERT: B 219 MET cc_start: 0.8232 (tpp) cc_final: 0.7894 (tpp) REVERT: B 250 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7221 (mp) REVERT: B 344 PHE cc_start: 0.7783 (m-80) cc_final: 0.7240 (t80) REVERT: B 367 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7547 (tt) REVERT: B 401 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 416 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6268 (ptt90) REVERT: B 417 ASP cc_start: 0.8997 (t0) cc_final: 0.8701 (t0) REVERT: B 479 LEU cc_start: 0.7573 (tt) cc_final: 0.7344 (tt) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 0.0705 time to fit residues: 16.2454 Evaluate side-chains 169 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.171022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129663 restraints weight = 10777.436| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.01 r_work: 0.3394 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 7824 Z= 0.137 Angle : 0.632 8.683 10622 Z= 0.314 Chirality : 0.040 0.161 1164 Planarity : 0.005 0.074 1272 Dihedral : 11.418 120.528 1214 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.03 % Allowed : 24.75 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.20 (0.30), residues: 894 helix: 1.57 (0.22), residues: 578 sheet: None (None), residues: 0 loop : -2.79 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.019 0.001 TYR A 465 PHE 0.012 0.001 PHE A 476 TRP 0.023 0.001 TRP A 461 HIS 0.004 0.001 HIS B 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 7824) covalent geometry : angle 0.63191 / 0.31 (10622) hydrogen bonds : bond 0.04267 / 2.81 ( 389) hydrogen bonds : angle 3.50258 / 2.58 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1402.21 seconds wall clock time: 24 minutes 46.68 seconds (1486.68 seconds total)