Starting phenix.real_space_refine on Fri Jul 3 13:04:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ulo_64265/07_2026/9ulo_64265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ulo_64265/07_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_64265/07_2026/9ulo_64265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ulo_64265/07_2026/9ulo_64265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ulo_64265/07_2026/9ulo_64265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ulo_64265/07_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): 0.01s 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: 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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 2.44, per 1000 atoms: 0.18 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: 1.10 Conformation dependent library (CDL) restraints added in 435.0 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: 0.20 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: 3.00 Time building geometry restraints manager: 1.48 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 3.080 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.050 Find NCS groups from input model: 0.130 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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/Z covalent geometry : bond 0.00208 / 0.10 ( 7036) covalent geometry : angle 0.48468 / 0.26 ( 9505) hydrogen bonds : bond 0.16157 / 11.00 ( 211) hydrogen bonds : angle 7.51839 / 5.37 ( 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 : 0.296 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: 0.1559 time to fit residues: 27.8049 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 : 0.379 ------------------------------------------------------------------------------- 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... ** A 126 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 ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.098449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081220 restraints weight = 70184.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084627 restraints weight = 34320.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086976 restraints weight = 21538.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.088663 restraints weight = 15516.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.089815 restraints weight = 12056.199| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7036 Z= 0.229 Angle : 0.578 6.378 9505 Z= 0.308 Chirality : 0.043 0.173 1035 Planarity : 0.004 0.037 1246 Dihedral : 4.466 22.808 908 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.30 % Favored : 94.46 % Rotamer: Outliers : 0.39 % Allowed : 7.28 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.29), residues: 849 helix: 1.88 (0.36), residues: 218 sheet: -1.15 (0.38), residues: 183 loop : -0.20 (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 0.010 0.002 TRP B 243 HIS 0.005 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 ( 7036) covalent geometry : angle 0.57752 / 0.31 ( 9505) hydrogen bonds : bond 0.03781 / 2.56 ( 211) hydrogen bonds : angle 5.84503 / 4.13 ( 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: 3 poor density : 112 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 TRP cc_start: 0.9015 (t-100) cc_final: 0.8718 (t-100) REVERT: A 342 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8714 (mm-30) REVERT: A 394 ASP cc_start: 0.8411 (m-30) cc_final: 0.8015 (t70) REVERT: B 228 PHE cc_start: 0.7705 (p90) cc_final: 0.7289 (p90) outliers start: 3 outliers final: 3 residues processed: 114 average time/residue: 0.1531 time to fit residues: 23.6316 Evaluate side-chains 103 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.097316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.080411 restraints weight = 69613.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083904 restraints weight = 33503.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086289 restraints weight = 20662.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.088003 restraints weight = 14664.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.089202 restraints weight = 11249.005| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7036 Z= 0.140 Angle : 0.498 3.967 9505 Z= 0.262 Chirality : 0.042 0.166 1035 Planarity : 0.004 0.039 1246 Dihedral : 4.240 25.525 908 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.88 % Rotamer: Outliers : 0.52 % Allowed : 9.23 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.30), residues: 849 helix: 2.24 (0.37), residues: 211 sheet: -1.27 (0.38), residues: 183 loop : -0.23 (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 0.018 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/Z covalent geometry : bond 0.00309 / 0.14 ( 7036) covalent geometry : angle 0.49825 / 0.26 ( 9505) hydrogen bonds : bond 0.03191 / 2.18 ( 211) hydrogen bonds : angle 5.38755 / 3.79 ( 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 108 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.316 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: A 342 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8699 (mm-30) REVERT: A 394 ASP cc_start: 0.8418 (m-30) cc_final: 0.8033 (t70) REVERT: B 75 CYS cc_start: 0.8963 (p) cc_final: 0.8711 (p) REVERT: B 228 PHE cc_start: 0.7858 (p90) cc_final: 0.7474 (p90) outliers start: 4 outliers final: 4 residues processed: 107 average time/residue: 0.1518 time to fit residues: 22.6350 Evaluate side-chains 105 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.092244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.075583 restraints weight = 71209.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078791 restraints weight = 35547.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.081056 restraints weight = 22620.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082631 restraints weight = 16368.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.083809 restraints weight = 12891.279| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7036 Z= 0.251 Angle : 0.578 4.256 9505 Z= 0.311 Chirality : 0.043 0.159 1035 Planarity : 0.004 0.039 1246 Dihedral : 4.811 23.634 908 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 1.82 % Allowed : 10.14 % Favored : 88.04 % 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: -0.59 (0.29), residues: 849 helix: 1.59 (0.36), residues: 212 sheet: -1.71 (0.36), residues: 190 loop : -0.70 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 292 TYR 0.011 0.002 TYR B 179 PHE 0.015 0.002 PHE B 54 TRP 0.009 0.002 TRP B 243 HIS 0.008 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.25 ( 7036) covalent geometry : angle 0.57828 / 0.31 ( 9505) hydrogen bonds : bond 0.03732 / 2.48 ( 211) hydrogen bonds : angle 5.65879 / 3.99 ( 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 105 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.231 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: 0.8953 (mm-30) cc_final: 0.8720 (mm-30) REVERT: A 394 ASP cc_start: 0.8418 (m-30) cc_final: 0.8174 (t70) REVERT: B 228 PHE cc_start: 0.8049 (p90) cc_final: 0.7673 (p90) outliers start: 14 outliers final: 12 residues processed: 99 average time/residue: 0.1263 time to fit residues: 18.1350 Evaluate side-chains 96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 317 HIS 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 324 ASP Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 376 PHE Chi-restraints excluded: chain B residue 396 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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 = 0.3834 r_free = 0.3834 target = 0.092989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076599 restraints weight = 71492.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.079920 restraints weight = 34524.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082231 restraints weight = 21368.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083843 restraints weight = 15278.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084959 restraints weight = 11824.533| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7036 Z= 0.138 Angle : 0.500 5.523 9505 Z= 0.262 Chirality : 0.042 0.163 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.471 25.057 908 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.29 % Rotamer: Outliers : 1.43 % Allowed : 11.44 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.29), residues: 849 helix: 1.92 (0.37), residues: 211 sheet: -1.86 (0.36), residues: 185 loop : -0.56 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.020 0.002 TYR A 179 PHE 0.013 0.001 PHE B 54 TRP 0.006 0.001 TRP B 243 HIS 0.005 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 7036) covalent geometry : angle 0.49988 / 0.26 ( 9505) hydrogen bonds : bond 0.03157 / 2.13 ( 211) hydrogen bonds : angle 5.34645 / 3.75 ( 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: 11 poor density : 89 time to evaluate : 0.263 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: 0.8969 (mm-30) cc_final: 0.8727 (mm-30) REVERT: A 394 ASP cc_start: 0.8518 (m-30) cc_final: 0.8187 (t70) REVERT: B 228 PHE cc_start: 0.8039 (p90) cc_final: 0.7686 (p90) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.1323 time to fit residues: 18.1669 Evaluate side-chains 93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.092375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076146 restraints weight = 70805.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.079405 restraints weight = 34402.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081711 restraints weight = 21372.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083311 restraints weight = 15252.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.084474 restraints weight = 11810.356| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3709 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= 0.146 Angle : 0.495 5.181 9505 Z= 0.260 Chirality : 0.042 0.160 1035 Planarity : 0.004 0.040 1246 Dihedral : 4.399 22.959 908 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.42 % Favored : 94.35 % Rotamer: Outliers : 1.82 % Allowed : 12.61 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 849 helix: 2.01 (0.36), residues: 211 sheet: -1.88 (0.37), residues: 185 loop : -0.58 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 292 TYR 0.010 0.001 TYR A 179 PHE 0.011 0.001 PHE B 54 TRP 0.006 0.001 TRP B 243 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 7036) covalent geometry : angle 0.49548 / 0.26 ( 9505) hydrogen bonds : bond 0.03034 / 2.02 ( 211) hydrogen bonds : angle 5.27192 / 3.70 ( 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 101 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.284 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 342 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8700 (mm-30) REVERT: A 394 ASP cc_start: 0.8510 (m-30) cc_final: 0.8188 (t70) REVERT: B 228 PHE cc_start: 0.8053 (p90) cc_final: 0.7685 (p90) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.1275 time to fit residues: 18.1493 Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 343 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: 1.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN B 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.093329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.076737 restraints weight = 69781.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.080077 restraints weight = 34379.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.082425 restraints weight = 21533.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.084063 restraints weight = 15433.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085224 restraints weight = 12007.813| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3756 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= 0.098 Angle : 0.482 7.440 9505 Z= 0.246 Chirality : 0.042 0.163 1035 Planarity : 0.003 0.040 1246 Dihedral : 4.153 21.638 908 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.48 % Favored : 95.29 % Rotamer: Outliers : 1.04 % Allowed : 13.26 % Favored : 85.70 % 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: -0.19 (0.30), residues: 849 helix: 2.22 (0.37), residues: 211 sheet: -1.76 (0.37), residues: 186 loop : -0.47 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 TYR 0.009 0.001 TYR A 179 PHE 0.014 0.001 PHE B 335 TRP 0.005 0.001 TRP B 108 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 7036) covalent geometry : angle 0.48182 / 0.25 ( 9505) hydrogen bonds : bond 0.02734 / 1.82 ( 211) hydrogen bonds : angle 5.03027 / 3.52 ( 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 97 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.401 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 342 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8697 (mm-30) REVERT: A 394 ASP cc_start: 0.8472 (m-30) cc_final: 0.8218 (t70) REVERT: B 228 PHE cc_start: 0.7941 (p90) cc_final: 0.7641 (p90) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.1679 time to fit residues: 22.0944 Evaluate side-chains 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 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 216 ILE 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: 1.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075494 restraints weight = 69520.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078742 restraints weight = 34385.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081021 restraints weight = 21664.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.082615 restraints weight = 15604.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083763 restraints weight = 12175.296| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7036 Z= 0.144 Angle : 0.497 6.452 9505 Z= 0.257 Chirality : 0.041 0.157 1035 Planarity : 0.003 0.040 1246 Dihedral : 4.269 21.559 908 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.65 % Favored : 94.23 % Rotamer: Outliers : 1.04 % Allowed : 13.52 % 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: -0.26 (0.30), residues: 849 helix: 2.22 (0.36), residues: 211 sheet: -1.83 (0.37), residues: 185 loop : -0.54 (0.29), residues: 453 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 0.014 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/Z covalent geometry : bond 0.00318 / 0.14 ( 7036) covalent geometry : angle 0.49719 / 0.26 ( 9505) hydrogen bonds : bond 0.02872 / 1.91 ( 211) hydrogen bonds : angle 5.15143 / 3.61 ( 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 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.384 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: A 342 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8681 (mm-30) REVERT: A 394 ASP cc_start: 0.8475 (m-30) cc_final: 0.8244 (t70) REVERT: B 228 PHE cc_start: 0.7986 (p90) cc_final: 0.7682 (p90) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.1519 time to fit residues: 19.6761 Evaluate side-chains 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 216 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3807 r_free = 0.3807 target = 0.091807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075832 restraints weight = 71632.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079110 restraints weight = 34565.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.081428 restraints weight = 21442.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.083025 restraints weight = 15236.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.084185 restraints weight = 11792.276| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7036 Z= 0.162 Angle : 0.519 7.315 9505 Z= 0.268 Chirality : 0.042 0.156 1035 Planarity : 0.004 0.041 1246 Dihedral : 4.383 20.892 908 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.24 % Favored : 93.64 % Rotamer: Outliers : 1.17 % Allowed : 13.78 % Favored : 85.05 % 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: -0.41 (0.29), residues: 849 helix: 2.13 (0.36), residues: 211 sheet: -1.88 (0.37), residues: 185 loop : -0.67 (0.29), residues: 453 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 0.016 0.001 PHE B 335 TRP 0.007 0.001 TRP B 243 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7036) covalent geometry : angle 0.51853 / 0.27 ( 9505) hydrogen bonds : bond 0.02976 / 1.97 ( 211) hydrogen bonds : angle 5.20669 / 3.65 ( 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 92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.394 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: A 278 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7784 (tp30) REVERT: A 342 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 376 PHE cc_start: 0.7468 (p90) cc_final: 0.7266 (p90) REVERT: A 394 ASP cc_start: 0.8531 (m-30) cc_final: 0.8310 (t70) REVERT: B 228 PHE cc_start: 0.8013 (p90) cc_final: 0.7743 (p90) outliers start: 9 outliers final: 7 residues processed: 89 average time/residue: 0.1601 time to fit residues: 20.4711 Evaluate side-chains 89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3838 r_free = 0.3838 target = 0.093251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077454 restraints weight = 70635.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.080749 restraints weight = 33919.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083079 restraints weight = 20920.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084693 restraints weight = 14839.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085860 restraints weight = 11387.374| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7036 Z= 0.099 Angle : 0.489 8.244 9505 Z= 0.248 Chirality : 0.042 0.164 1035 Planarity : 0.003 0.040 1246 Dihedral : 4.149 19.977 908 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 0.91 % Allowed : 14.43 % Favored : 84.66 % 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: -0.23 (0.30), residues: 849 helix: 2.41 (0.37), residues: 205 sheet: -1.69 (0.36), residues: 191 loop : -0.61 (0.29), residues: 453 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 0.010 0.001 PHE B 381 TRP 0.006 0.001 TRP B 108 HIS 0.006 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7036) covalent geometry : angle 0.48890 / 0.25 ( 9505) hydrogen bonds : bond 0.02662 / 1.77 ( 211) hydrogen bonds : angle 4.98156 / 3.49 ( 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 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.399 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: 0.8937 (mm-30) cc_final: 0.8679 (mm-30) REVERT: A 376 PHE cc_start: 0.7441 (p90) cc_final: 0.7081 (p90) REVERT: B 228 PHE cc_start: 0.7920 (p90) cc_final: 0.7654 (p90) outliers start: 7 outliers final: 6 residues processed: 88 average time/residue: 0.1631 time to fit residues: 20.4540 Evaluate side-chains 86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 216 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 5.9990 chunk 57 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3858 r_free = 0.3858 target = 0.094045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077779 restraints weight = 69714.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081123 restraints weight = 33682.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083504 restraints weight = 20889.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085159 restraints weight = 14827.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.086377 restraints weight = 11438.136| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7036 Z= 0.093 Angle : 0.483 8.370 9505 Z= 0.243 Chirality : 0.042 0.164 1035 Planarity : 0.003 0.040 1246 Dihedral : 4.045 19.672 908 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.06 % Favored : 94.82 % Rotamer: Outliers : 1.17 % Allowed : 14.17 % Favored : 84.66 % 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 (0.30), residues: 849 helix: 2.48 (0.37), residues: 205 sheet: -1.59 (0.36), residues: 191 loop : -0.55 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.015 0.001 TYR A 369 PHE 0.016 0.001 PHE B 335 TRP 0.006 0.001 TRP B 108 HIS 0.007 0.001 HIS B 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.09 ( 7036) covalent geometry : angle 0.48268 / 0.24 ( 9505) hydrogen bonds : bond 0.02512 / 1.68 ( 211) hydrogen bonds : angle 4.86673 / 3.41 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.77 seconds wall clock time: 40 minutes 8.70 seconds (2408.70 seconds total)