Starting phenix.real_space_refine on Sun May 3 15:48:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ulo_64265/05_2026/9ulo_64265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ulo_64265/05_2026/9ulo_64265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ulo_64265/05_2026/9ulo_64265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ulo_64265/05_2026/9ulo_64265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ulo_64265/05_2026/9ulo_64265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ulo_64265/05_2026/9ulo_64265.map" } resolution = 3.91 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= 0.002 sd= 0.038 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 S 30 5.16 5 C 4386 2.51 5 N 1195 2.21 5 O 1263 1.98 5 H 6793 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13671 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6379 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 20, 'TRANS': 378} Chain: "B" Number of atoms: 6368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6368 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 20, 'TRANS': 377} Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 920 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.15, per 1000 atoms: 0.16 Number of scatterers: 13671 At special positions: 0 Unit cell: (106.02, 91.14, 88.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 30 16.00 O 1263 8.00 N 1195 7.00 C 4386 6.00 H 6793 1.00 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: 0.84 Conformation dependent library (CDL) restraints added in 319.7 milliseconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 29.0% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 96 through 101 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.685A pdb=" N VAL A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.262A pdb=" N GLY A 353 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 68 through 84 removed outlier: 3.703A pdb=" N MET B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 102 removed outlier: 3.582A pdb=" N ASN B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.729A pdb=" N TRP B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 removed outlier: 3.883A pdb=" N VAL B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 327 through 352 Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 391 through 394 removed outlier: 3.578A pdb=" N ASP B 394 " --> pdb=" O ASN B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 394' Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.562A pdb=" N VAL A 122 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS A 14 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 56 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 16 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.218A pdb=" N VAL A 241 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 263 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 252 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.400A pdb=" N ILE A 162 " --> pdb=" O THR A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 313 removed outlier: 6.470A pdb=" N PHE A 308 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ARG A 366 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU A 310 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASP A 368 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 312 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N HIS A 397 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU A 365 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 399 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 367 " --> pdb=" O PHE A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.592A pdb=" N VAL B 122 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 55 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B 14 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU B 56 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 16 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.592A pdb=" N VAL B 122 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE B 55 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS B 14 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU B 56 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 16 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 93 removed outlier: 6.172A pdb=" N VAL B 241 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE B 263 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA B 252 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.688A pdb=" N THR B 199 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 164 " --> pdb=" O THR B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AB1, first strand: chain 'B' and resid 307 through 313 removed outlier: 6.650A pdb=" N PHE B 308 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ARG B 366 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B 310 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP B 368 " --> pdb=" O GLU B 310 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 312 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 399 " --> pdb=" O VAL B 367 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 579 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: 2.55 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6781 1.03 - 1.23: 12 1.23 - 1.42: 2968 1.42 - 1.62: 4020 1.62 - 1.81: 48 Bond restraints: 13829 Sorted by residual: bond pdb=" CB GLU C 658 " pdb=" CG GLU C 658 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CA PHE C 659 " pdb=" CB PHE C 659 " ideal model delta sigma weight residual 1.524 1.537 -0.014 1.31e-02 5.83e+03 1.07e+00 bond pdb=" CA ILE B 164 " pdb=" CB ILE B 164 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 8.35e-01 bond pdb=" C ASN A 322 " pdb=" O ASN A 322 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.85e-01 bond pdb=" CA VAL B 271 " pdb=" CB VAL B 271 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.36e-02 5.41e+03 7.75e-01 ... (remaining 13824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 23675 1.07 - 2.15: 1258 2.15 - 3.22: 51 3.22 - 4.30: 30 4.30 - 5.37: 5 Bond angle restraints: 25019 Sorted by residual: angle pdb=" N SER C 667 " pdb=" CA SER C 667 " pdb=" C SER C 667 " ideal model delta sigma weight residual 113.18 108.41 4.77 1.33e+00 5.65e-01 1.29e+01 angle pdb=" C PHE C 659 " pdb=" CA PHE C 659 " pdb=" CB PHE C 659 " ideal model delta sigma weight residual 111.50 107.46 4.04 1.29e+00 6.01e-01 9.79e+00 angle pdb=" N SER C 661 " pdb=" CA SER C 661 " pdb=" C SER C 661 " ideal model delta sigma weight residual 108.58 113.95 -5.37 1.82e+00 3.02e-01 8.71e+00 angle pdb=" CB GLU C 658 " pdb=" CG GLU C 658 " pdb=" CD GLU C 658 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.70e+00 3.46e-01 7.49e+00 angle pdb=" N GLU A 341 " pdb=" CA GLU A 341 " pdb=" CB GLU A 341 " ideal model delta sigma weight residual 110.12 113.69 -3.57 1.47e+00 4.63e-01 5.90e+00 ... (remaining 25014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5993 17.54 - 35.08: 378 35.08 - 52.62: 108 52.62 - 70.16: 20 70.16 - 87.70: 3 Dihedral angle restraints: 6502 sinusoidal: 3534 harmonic: 2968 Sorted by residual: dihedral pdb=" CA GLN B 97 " pdb=" CB GLN B 97 " pdb=" CG GLN B 97 " pdb=" CD GLN B 97 " ideal model delta sinusoidal sigma weight residual 60.00 113.73 -53.73 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ASP B 235 " pdb=" CB ASP B 235 " pdb=" CG ASP B 235 " pdb=" OD1 ASP B 235 " ideal model delta sinusoidal sigma weight residual -30.00 -81.54 51.54 1 2.00e+01 2.50e-03 9.07e+00 dihedral pdb=" CA ASN C 666 " pdb=" C ASN C 666 " pdb=" N SER C 667 " pdb=" CA SER C 667 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.98e+00 ... (remaining 6499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 670 0.031 - 0.062: 248 0.062 - 0.093: 47 0.093 - 0.124: 62 0.124 - 0.155: 8 Chirality restraints: 1035 Sorted by residual: chirality pdb=" CA ILE A 184 " pdb=" N ILE A 184 " pdb=" C ILE A 184 " pdb=" CB ILE A 184 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE B 184 " pdb=" N ILE B 184 " pdb=" C ILE B 184 " pdb=" CB ILE B 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CB ILE B 320 " pdb=" CA ILE B 320 " pdb=" CG1 ILE B 320 " pdb=" CG2 ILE B 320 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1032 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 658 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C GLU C 658 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU C 658 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 659 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 45 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C ARG A 45 " -0.028 2.00e-02 2.50e+03 pdb=" O ARG A 45 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 46 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 184 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 185 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.020 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 296 2.10 - 2.72: 23982 2.72 - 3.35: 40408 3.35 - 3.97: 51011 3.97 - 4.60: 79328 Nonbonded interactions: 195025 Sorted by model distance: nonbonded pdb="MN MN A 801 " pdb="MN MN A 802 " model vdw 1.472 1.600 nonbonded pdb=" H ASN B 110 " pdb=" OD1 ASN B 151 " model vdw 1.509 2.450 nonbonded pdb=" OD2 ASP B 29 " pdb=" H ARG B 32 " model vdw 1.582 2.450 nonbonded pdb="HH11 ARG C 660 " pdb=" H SER C 661 " model vdw 1.599 2.100 nonbonded pdb="HH11 ARG B 305 " pdb=" O LYS B 360 " model vdw 1.605 2.450 ... (remaining 195020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 4 through 802)) 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 group one per residue 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: 1.680 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.002 0.032 7036 Z= 0.099 Angle : 0.485 5.371 9505 Z= 0.262 Chirality : 0.041 0.155 1035 Planarity : 0.003 0.035 1246 Dihedral : 12.165 87.698 2632 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.42 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.72 (0.30), residues: 849 helix: 2.37 (0.38), residues: 211 sheet: -0.23 (0.39), residues: 188 loop : -0.05 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 364 TYR 0.005 0.001 TYR A 111 PHE 0.015 0.001 PHE B 335 TRP 0.003 0.001 TRP B 108 HIS 0.002 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 7036) covalent geometry : angle 0.48468 ( 9505) hydrogen bonds : bond 0.16157 ( 211) hydrogen bonds : angle 7.51839 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8646 (mm-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1748 time to fit residues: 30.8095 Evaluate side-chains 102 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 ASN A 354 ASN ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.097608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080466 restraints weight = 69267.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083833 restraints weight = 34773.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086208 restraints weight = 22186.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087906 restraints weight = 16028.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.089114 restraints weight = 12499.547| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7036 Z= 0.236 Angle : 0.584 6.748 9505 Z= 0.312 Chirality : 0.043 0.171 1035 Planarity : 0.004 0.034 1246 Dihedral : 4.558 23.552 908 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.54 % Favored : 94.23 % Rotamer: Outliers : 0.52 % Allowed : 7.41 % Favored : 92.07 % 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 (0.29), residues: 849 helix: 1.86 (0.36), residues: 218 sheet: -1.19 (0.37), residues: 183 loop : -0.24 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 80 TYR 0.010 0.002 TYR B 179 PHE 0.013 0.002 PHE B 237 TRP 0.011 0.002 TRP B 243 HIS 0.003 0.001 HIS A 129 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 7036) covalent geometry : angle 0.58433 ( 9505) hydrogen bonds : bond 0.03767 ( 211) hydrogen bonds : angle 5.82649 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 TRP cc_start: 0.9010 (t-100) cc_final: 0.8744 (t-100) REVERT: A 342 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8688 (mm-30) REVERT: A 394 ASP cc_start: 0.8343 (m-30) cc_final: 0.8012 (t70) REVERT: B 228 PHE cc_start: 0.7637 (p90) cc_final: 0.7256 (p90) outliers start: 4 outliers final: 4 residues processed: 114 average time/residue: 0.1727 time to fit residues: 26.9138 Evaluate side-chains 103 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 324 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS B 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.097227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.080148 restraints weight = 68037.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.083598 restraints weight = 33874.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085989 restraints weight = 21399.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.087704 restraints weight = 15390.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088918 restraints weight = 11960.218| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7036 Z= 0.129 Angle : 0.495 3.980 9505 Z= 0.259 Chirality : 0.042 0.166 1035 Planarity : 0.004 0.039 1246 Dihedral : 4.242 25.361 908 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.77 % Favored : 96.00 % Rotamer: Outliers : 0.78 % Allowed : 9.10 % Favored : 90.12 % 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: 0.20 (0.30), residues: 849 helix: 2.29 (0.37), residues: 211 sheet: -1.26 (0.37), residues: 183 loop : -0.22 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.013 0.001 TYR A 179 PHE 0.017 0.001 PHE B 54 TRP 0.005 0.001 TRP B 243 HIS 0.008 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7036) covalent geometry : angle 0.49514 ( 9505) hydrogen bonds : bond 0.03133 ( 211) hydrogen bonds : angle 5.34737 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 TRP cc_start: 0.8943 (t-100) cc_final: 0.8671 (t-100) REVERT: A 342 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8683 (mm-30) REVERT: A 394 ASP cc_start: 0.8393 (m-30) cc_final: 0.8052 (t70) REVERT: B 75 CYS cc_start: 0.8963 (p) cc_final: 0.8714 (p) REVERT: B 228 PHE cc_start: 0.7817 (p90) cc_final: 0.7448 (p90) outliers start: 6 outliers final: 4 residues processed: 105 average time/residue: 0.1600 time to fit residues: 23.4595 Evaluate side-chains 104 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.095248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078285 restraints weight = 68969.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081623 restraints weight = 35128.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083962 restraints weight = 22386.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085591 restraints weight = 16210.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086810 restraints weight = 12697.428| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7036 Z= 0.173 Angle : 0.510 4.094 9505 Z= 0.269 Chirality : 0.042 0.162 1035 Planarity : 0.004 0.038 1246 Dihedral : 4.418 26.703 908 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 1.69 % Allowed : 9.88 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.12 (0.29), residues: 849 helix: 2.04 (0.37), residues: 212 sheet: -1.51 (0.37), residues: 183 loop : -0.42 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.022 0.002 TYR A 179 PHE 0.016 0.001 PHE B 54 TRP 0.006 0.001 TRP B 243 HIS 0.009 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7036) covalent geometry : angle 0.51018 ( 9505) hydrogen bonds : bond 0.03097 ( 211) hydrogen bonds : angle 5.34101 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8693 (mm-30) REVERT: A 394 ASP cc_start: 0.8414 (m-30) cc_final: 0.8153 (t70) REVERT: B 228 PHE cc_start: 0.7915 (p90) cc_final: 0.7574 (p90) outliers start: 13 outliers final: 11 residues processed: 103 average time/residue: 0.1414 time to fit residues: 20.9850 Evaluate side-chains 99 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.095797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.078546 restraints weight = 68959.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081953 restraints weight = 35036.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.084329 restraints weight = 22327.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086038 restraints weight = 16149.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086928 restraints weight = 12607.483| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7036 Z= 0.115 Angle : 0.475 4.925 9505 Z= 0.245 Chirality : 0.041 0.164 1035 Planarity : 0.003 0.039 1246 Dihedral : 4.204 23.402 908 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.24 % Favored : 95.52 % Rotamer: Outliers : 1.17 % Allowed : 10.66 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.30), residues: 849 helix: 2.08 (0.37), residues: 217 sheet: -1.52 (0.37), residues: 183 loop : -0.29 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.009 0.001 TYR A 179 PHE 0.012 0.001 PHE B 54 TRP 0.005 0.001 TRP B 243 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7036) covalent geometry : angle 0.47463 ( 9505) hydrogen bonds : bond 0.02761 ( 211) hydrogen bonds : angle 5.10604 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8693 (mm-30) REVERT: A 394 ASP cc_start: 0.8407 (m-30) cc_final: 0.8148 (t70) REVERT: B 228 PHE cc_start: 0.7901 (p90) cc_final: 0.7558 (p90) outliers start: 9 outliers final: 9 residues processed: 97 average time/residue: 0.1398 time to fit residues: 19.6857 Evaluate side-chains 98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN B 73 HIS ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.092433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075466 restraints weight = 68545.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078716 restraints weight = 35437.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081006 restraints weight = 22924.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.082614 restraints weight = 16784.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.083771 restraints weight = 13238.973| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7036 Z= 0.195 Angle : 0.538 5.390 9505 Z= 0.285 Chirality : 0.042 0.156 1035 Planarity : 0.004 0.039 1246 Dihedral : 4.602 21.965 908 Min Nonbonded Distance : 1.307 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 1.82 % Allowed : 11.83 % Favored : 86.35 % 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: -0.46 (0.29), residues: 849 helix: 1.85 (0.36), residues: 212 sheet: -1.88 (0.35), residues: 192 loop : -0.57 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 292 TYR 0.009 0.002 TYR A 179 PHE 0.016 0.002 PHE B 335 TRP 0.008 0.002 TRP B 210 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 7036) covalent geometry : angle 0.53780 ( 9505) hydrogen bonds : bond 0.03336 ( 211) hydrogen bonds : angle 5.37456 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8700 (mm-30) REVERT: B 228 PHE cc_start: 0.8024 (p90) cc_final: 0.7667 (p90) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.1372 time to fit residues: 18.4192 Evaluate side-chains 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.093566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.076911 restraints weight = 67649.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080227 restraints weight = 34223.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082541 restraints weight = 21865.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.084215 restraints weight = 15846.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.085423 restraints weight = 12331.304| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7036 Z= 0.105 Angle : 0.481 5.792 9505 Z= 0.248 Chirality : 0.042 0.163 1035 Planarity : 0.004 0.038 1246 Dihedral : 4.282 20.425 908 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.29 % Rotamer: Outliers : 1.30 % Allowed : 12.61 % Favored : 86.09 % 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: -0.21 (0.30), residues: 849 helix: 2.16 (0.37), residues: 211 sheet: -1.79 (0.37), residues: 183 loop : -0.47 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.007 0.001 TYR A 179 PHE 0.014 0.001 PHE B 335 TRP 0.005 0.001 TRP B 108 HIS 0.008 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7036) covalent geometry : angle 0.48105 ( 9505) hydrogen bonds : bond 0.02780 ( 211) hydrogen bonds : angle 5.07610 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8693 (mm-30) REVERT: B 228 PHE cc_start: 0.7914 (p90) cc_final: 0.7604 (p90) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.1520 time to fit residues: 19.7500 Evaluate side-chains 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.093137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076355 restraints weight = 67991.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079665 restraints weight = 34825.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081986 restraints weight = 22305.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083599 restraints weight = 16204.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084793 restraints weight = 12724.784| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7036 Z= 0.126 Angle : 0.492 8.585 9505 Z= 0.252 Chirality : 0.041 0.160 1035 Planarity : 0.003 0.038 1246 Dihedral : 4.277 20.365 908 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.06 % Favored : 94.70 % Rotamer: Outliers : 1.43 % Allowed : 12.35 % Favored : 86.22 % 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: -0.22 (0.29), residues: 849 helix: 2.22 (0.37), residues: 211 sheet: -1.82 (0.37), residues: 183 loop : -0.50 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 202 TYR 0.007 0.001 TYR A 179 PHE 0.018 0.001 PHE B 13 TRP 0.005 0.001 TRP B 243 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7036) covalent geometry : angle 0.49229 ( 9505) hydrogen bonds : bond 0.02784 ( 211) hydrogen bonds : angle 5.09394 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7736 (tp30) REVERT: A 342 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8676 (mm-30) REVERT: B 228 PHE cc_start: 0.7915 (p90) cc_final: 0.7562 (p90) outliers start: 11 outliers final: 8 residues processed: 88 average time/residue: 0.1535 time to fit residues: 19.2239 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.094088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.077431 restraints weight = 67869.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.080798 restraints weight = 33946.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083173 restraints weight = 21530.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084849 restraints weight = 15478.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086054 restraints weight = 12016.452| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7036 Z= 0.091 Angle : 0.472 7.620 9505 Z= 0.238 Chirality : 0.042 0.164 1035 Planarity : 0.003 0.039 1246 Dihedral : 4.087 19.427 908 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 1.04 % Allowed : 12.74 % Favored : 86.22 % 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: -0.11 (0.30), residues: 849 helix: 2.44 (0.37), residues: 205 sheet: -1.72 (0.36), residues: 186 loop : -0.46 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 TYR 0.007 0.001 TYR A 179 PHE 0.012 0.001 PHE B 13 TRP 0.006 0.001 TRP B 108 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 7036) covalent geometry : angle 0.47196 ( 9505) hydrogen bonds : bond 0.02561 ( 211) hydrogen bonds : angle 4.88808 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8671 (mm-30) REVERT: B 228 PHE cc_start: 0.7788 (p90) cc_final: 0.7530 (p90) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.1664 time to fit residues: 20.4916 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.091604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.075226 restraints weight = 68465.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078470 restraints weight = 35042.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080756 restraints weight = 22434.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082309 restraints weight = 16287.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083484 restraints weight = 12806.497| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7036 Z= 0.204 Angle : 0.533 7.453 9505 Z= 0.280 Chirality : 0.042 0.168 1035 Planarity : 0.004 0.039 1246 Dihedral : 4.521 20.061 908 Min Nonbonded Distance : 1.308 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 0.78 % Allowed : 13.00 % Favored : 86.22 % 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: -0.51 (0.29), residues: 849 helix: 2.02 (0.36), residues: 212 sheet: -1.99 (0.35), residues: 194 loop : -0.66 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 80 TYR 0.009 0.002 TYR A 82 PHE 0.014 0.002 PHE B 37 TRP 0.010 0.002 TRP B 210 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 7036) covalent geometry : angle 0.53326 ( 9505) hydrogen bonds : bond 0.03187 ( 211) hydrogen bonds : angle 5.26003 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7865 (tp30) REVERT: A 342 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8663 (mm-30) REVERT: B 228 PHE cc_start: 0.7955 (p90) cc_final: 0.7697 (p90) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1537 time to fit residues: 18.6841 Evaluate side-chains 83 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 376 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076849 restraints weight = 70005.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.080192 restraints weight = 35150.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082600 restraints weight = 22483.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.084236 restraints weight = 16287.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.085475 restraints weight = 12748.078| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7036 Z= 0.101 Angle : 0.483 8.125 9505 Z= 0.245 Chirality : 0.041 0.163 1035 Planarity : 0.004 0.039 1246 Dihedral : 4.212 19.265 908 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.83 % Favored : 95.05 % Rotamer: Outliers : 0.78 % Allowed : 13.78 % Favored : 85.44 % 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: -0.28 (0.29), residues: 849 helix: 2.26 (0.37), residues: 211 sheet: -1.78 (0.35), residues: 190 loop : -0.61 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 TYR 0.006 0.001 TYR A 179 PHE 0.017 0.001 PHE B 335 TRP 0.005 0.001 TRP B 108 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7036) covalent geometry : angle 0.48348 ( 9505) hydrogen bonds : bond 0.02673 ( 211) hydrogen bonds : angle 4.98379 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.23 seconds wall clock time: 39 minutes 56.20 seconds (2396.20 seconds total)