Starting phenix.real_space_refine on Tue Feb 3 14:48:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mm5_48385/02_2026/9mm5_48385.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mm5_48385/02_2026/9mm5_48385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mm5_48385/02_2026/9mm5_48385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mm5_48385/02_2026/9mm5_48385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mm5_48385/02_2026/9mm5_48385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mm5_48385/02_2026/9mm5_48385.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2595 2.51 5 N 659 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3946 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 411 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 719 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 3, 'TRP:plan': 2, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "R" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2816 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 5, 'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 0.83, per 1000 atoms: 0.21 Number of scatterers: 3946 At special positions: 0 Unit cell: (65.25, 69.75, 112.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 664 8.00 N 659 7.00 C 2595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 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: 0.19 Conformation dependent library (CDL) restraints added in 109.3 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 77.9% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 1 through 20 Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 42 through 65 removed outlier: 3.952A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.977A pdb=" N GLU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 81 removed outlier: 4.506A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU E 78 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 100 Processing helix chain 'E' and resid 118 through 142 removed outlier: 3.889A pdb=" N PHE E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.203A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.572A pdb=" N ASN R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 166 removed outlier: 3.663A pdb=" N PHE R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.664A pdb=" N VAL R 205 " --> pdb=" O ASN R 201 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 243 removed outlier: 4.277A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER R 215 " --> pdb=" O SER R 211 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN R 216 " --> pdb=" O CYS R 212 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR R 227 " --> pdb=" O MET R 223 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL R 243 " --> pdb=" O THR R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.615A pdb=" N ALA R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.640A pdb=" N ILE R 284 " --> pdb=" O ASN R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 319 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 319 through 324 Processing helix chain 'R' and resid 325 through 347 removed outlier: 3.823A pdb=" N LEU R 330 " --> pdb=" O ALA R 326 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR R 331 " --> pdb=" O GLU R 327 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS R 333 " --> pdb=" O ASN R 329 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA R 334 " --> pdb=" O LEU R 330 " (cutoff:3.500A) Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 347 through 352 Processing helix chain 'R' and resid 357 through 375 removed outlier: 4.179A pdb=" N ALA R 361 " --> pdb=" O GLU R 357 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL R 364 " --> pdb=" O ILE R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 386 Processing helix chain 'R' and resid 388 through 402 removed outlier: 3.543A pdb=" N GLN R 401 " --> pdb=" O ARG R 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 82 through 87 284 hydrogen bonds defined for protein. 843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1228 1.35 - 1.47: 1088 1.47 - 1.58: 1701 1.58 - 1.70: 0 1.70 - 1.82: 37 Bond restraints: 4054 Sorted by residual: bond pdb=" C ILE R 352 " pdb=" N PRO R 353 " ideal model delta sigma weight residual 1.333 1.357 -0.024 7.80e-03 1.64e+04 9.20e+00 bond pdb=" N GLU E 78 " pdb=" CA GLU E 78 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" N LYS E 79 " pdb=" CA LYS E 79 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.59e+00 bond pdb=" N THR E 73 " pdb=" CA THR E 73 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.58e+00 bond pdb=" N CYS E 72 " pdb=" CA CYS E 72 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.53e+00 ... (remaining 4049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 5330 1.56 - 3.13: 181 3.13 - 4.69: 26 4.69 - 6.25: 8 6.25 - 7.81: 6 Bond angle restraints: 5551 Sorted by residual: angle pdb=" N GLN A 16 " pdb=" CA GLN A 16 " pdb=" CB GLN A 16 " ideal model delta sigma weight residual 110.12 115.29 -5.17 1.47e+00 4.63e-01 1.24e+01 angle pdb=" CA TYR E 66 " pdb=" CB TYR E 66 " pdb=" CG TYR E 66 " ideal model delta sigma weight residual 113.90 119.75 -5.85 1.80e+00 3.09e-01 1.05e+01 angle pdb=" C VAL R 242 " pdb=" N VAL R 243 " pdb=" CA VAL R 243 " ideal model delta sigma weight residual 122.97 119.80 3.17 9.80e-01 1.04e+00 1.05e+01 angle pdb=" CA GLN R 45 " pdb=" CB GLN R 45 " pdb=" CG GLN R 45 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" C VAL E 124 " pdb=" N VAL E 125 " pdb=" CA VAL E 125 " ideal model delta sigma weight residual 120.33 122.63 -2.30 8.00e-01 1.56e+00 8.29e+00 ... (remaining 5546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.07: 2029 12.07 - 24.15: 209 24.15 - 36.22: 65 36.22 - 48.30: 12 48.30 - 60.37: 8 Dihedral angle restraints: 2323 sinusoidal: 750 harmonic: 1573 Sorted by residual: dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 41.94 51.06 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA ARG R 355 " pdb=" C ARG R 355 " pdb=" N PRO R 356 " pdb=" CA PRO R 356 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA TYR E 100 " pdb=" C TYR E 100 " pdb=" N PHE E 101 " pdb=" CA PHE E 101 " ideal model delta harmonic sigma weight residual -180.00 -158.46 -21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 433 0.038 - 0.076: 172 0.076 - 0.114: 35 0.114 - 0.152: 5 0.152 - 0.190: 1 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA TYR R 49 " pdb=" N TYR R 49 " pdb=" C TYR R 49 " pdb=" CB TYR R 49 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.02e-01 chirality pdb=" CA MET E 76 " pdb=" N MET E 76 " pdb=" C MET E 76 " pdb=" CB MET E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE R 384 " pdb=" N PHE R 384 " pdb=" C PHE R 384 " pdb=" CB PHE R 384 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 643 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 66 " -0.028 2.00e-02 2.50e+03 1.93e-02 7.48e+00 pdb=" CG TYR E 66 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 66 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 66 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 66 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR E 66 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 66 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 29 " -0.013 2.00e-02 2.50e+03 1.48e-02 4.40e+00 pdb=" CG TYR A 29 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 29 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 29 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 29 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 29 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 29 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 29 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 37 " -0.010 2.00e-02 2.50e+03 1.51e-02 4.01e+00 pdb=" CG PHE A 37 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 37 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 37 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 37 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 37 " -0.001 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1252 2.83 - 3.35: 4058 3.35 - 3.87: 6417 3.87 - 4.38: 6699 4.38 - 4.90: 11479 Nonbonded interactions: 29905 Sorted by model distance: nonbonded pdb=" O VAL A 19 " pdb=" NH1 ARG R 38 " model vdw 2.317 3.120 nonbonded pdb=" OH TYR E 66 " pdb=" OE1 GLN R 45 " model vdw 2.362 3.040 nonbonded pdb=" O PHE E 83 " pdb=" NH2 ARG R 119 " model vdw 2.398 3.120 nonbonded pdb=" N GLY R 81 " pdb=" O CYS R 105 " model vdw 2.446 3.120 nonbonded pdb=" N CYS R 88 " pdb=" O GLU R 99 " model vdw 2.506 3.120 ... (remaining 29900 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.350 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.003 0.031 4060 Z= 0.205 Angle : 0.698 7.815 5563 Z= 0.425 Chirality : 0.041 0.190 646 Planarity : 0.004 0.035 690 Dihedral : 11.821 60.373 1285 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.38), residues: 522 helix: 2.02 (0.28), residues: 352 sheet: 2.49 (1.44), residues: 12 loop : -0.74 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 112 TYR 0.045 0.002 TYR E 66 PHE 0.034 0.002 PHE A 37 TRP 0.011 0.001 TRP E 139 HIS 0.007 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4054) covalent geometry : angle 0.69715 ( 5551) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.85336 ( 12) hydrogen bonds : bond 0.15550 ( 284) hydrogen bonds : angle 4.90013 ( 843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.9179 (mmm) cc_final: 0.8829 (mmm) REVERT: A 15 LEU cc_start: 0.8968 (tp) cc_final: 0.8625 (tp) REVERT: A 29 TYR cc_start: 0.8725 (m-80) cc_final: 0.8423 (m-80) REVERT: E 72 CYS cc_start: 0.7156 (t) cc_final: 0.6908 (t) REVERT: R 99 GLU cc_start: 0.8653 (tp30) cc_final: 0.8420 (tm-30) REVERT: R 390 GLU cc_start: 0.8569 (mp0) cc_final: 0.8305 (mp0) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0551 time to fit residues: 4.9037 Evaluate side-chains 56 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS R 114 HIS R 187 ASN R 226 ASN ** R 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.104171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067429 restraints weight = 10110.764| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.76 r_work: 0.2928 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4060 Z= 0.137 Angle : 0.569 7.582 5563 Z= 0.308 Chirality : 0.039 0.142 646 Planarity : 0.004 0.032 690 Dihedral : 4.600 23.420 564 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.12 % Allowed : 9.27 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.26 (0.38), residues: 522 helix: 2.40 (0.28), residues: 365 sheet: 1.89 (1.30), residues: 12 loop : -1.00 (0.53), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 38 TYR 0.014 0.001 TYR A 29 PHE 0.048 0.002 PHE A 37 TRP 0.013 0.001 TRP E 59 HIS 0.006 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4054) covalent geometry : angle 0.56885 ( 5551) SS BOND : bond 0.00204 ( 6) SS BOND : angle 0.76912 ( 12) hydrogen bonds : bond 0.05126 ( 284) hydrogen bonds : angle 3.90405 ( 843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9438 (mmm) cc_final: 0.9027 (mmm) REVERT: A 15 LEU cc_start: 0.8994 (tp) cc_final: 0.8744 (tp) REVERT: A 29 TYR cc_start: 0.8922 (m-80) cc_final: 0.8522 (m-80) REVERT: E 36 LEU cc_start: 0.9655 (mt) cc_final: 0.9424 (tp) REVERT: E 48 MET cc_start: 0.6525 (tpt) cc_final: 0.6291 (mmm) REVERT: E 92 PHE cc_start: 0.9147 (t80) cc_final: 0.8750 (t80) REVERT: R 38 ARG cc_start: 0.7916 (ptp-110) cc_final: 0.7608 (ptp-110) REVERT: R 99 GLU cc_start: 0.8689 (tp30) cc_final: 0.8376 (tm-30) REVERT: R 390 GLU cc_start: 0.9296 (mp0) cc_final: 0.8923 (mp0) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.0426 time to fit residues: 4.1400 Evaluate side-chains 62 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain R residue 195 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.104087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067779 restraints weight = 9994.823| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.68 r_work: 0.2925 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4060 Z= 0.121 Angle : 0.538 6.625 5563 Z= 0.287 Chirality : 0.039 0.230 646 Planarity : 0.003 0.036 690 Dihedral : 4.433 22.682 564 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.40 % Allowed : 12.36 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.35 (0.38), residues: 522 helix: 2.46 (0.27), residues: 368 sheet: 2.07 (1.39), residues: 12 loop : -1.02 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 112 TYR 0.014 0.001 TYR E 66 PHE 0.015 0.001 PHE A 37 TRP 0.013 0.001 TRP E 59 HIS 0.008 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 4054) covalent geometry : angle 0.53784 ( 5551) SS BOND : bond 0.00177 ( 6) SS BOND : angle 0.58065 ( 12) hydrogen bonds : bond 0.04518 ( 284) hydrogen bonds : angle 3.68844 ( 843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9454 (mmm) cc_final: 0.9025 (mmm) REVERT: A 29 TYR cc_start: 0.9026 (m-80) cc_final: 0.8629 (m-80) REVERT: E 36 LEU cc_start: 0.9636 (mt) cc_final: 0.9417 (tp) REVERT: E 48 MET cc_start: 0.6659 (tpt) cc_final: 0.6345 (mmm) REVERT: E 92 PHE cc_start: 0.9166 (t80) cc_final: 0.8811 (t80) REVERT: E 113 ASP cc_start: 0.9240 (m-30) cc_final: 0.9019 (m-30) REVERT: R 38 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7541 (ptp-110) REVERT: R 390 GLU cc_start: 0.9318 (mp0) cc_final: 0.8973 (mp0) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.0721 time to fit residues: 6.2619 Evaluate side-chains 64 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.0970 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS R 324 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.104278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067763 restraints weight = 10117.660| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.72 r_work: 0.2938 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4060 Z= 0.115 Angle : 0.522 7.840 5563 Z= 0.277 Chirality : 0.038 0.204 646 Planarity : 0.003 0.031 690 Dihedral : 4.278 22.609 564 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.81 % Allowed : 14.33 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.44 (0.39), residues: 522 helix: 2.55 (0.27), residues: 377 sheet: 2.45 (1.45), residues: 12 loop : -1.37 (0.56), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 112 TYR 0.016 0.001 TYR R 91 PHE 0.012 0.001 PHE E 92 TRP 0.015 0.001 TRP E 59 HIS 0.009 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4054) covalent geometry : angle 0.52156 ( 5551) SS BOND : bond 0.00412 ( 6) SS BOND : angle 0.54888 ( 12) hydrogen bonds : bond 0.04123 ( 284) hydrogen bonds : angle 3.58848 ( 843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9473 (mmm) cc_final: 0.9228 (mmm) REVERT: A 29 TYR cc_start: 0.9051 (m-80) cc_final: 0.8645 (m-80) REVERT: E 36 LEU cc_start: 0.9607 (mt) cc_final: 0.9401 (tp) REVERT: E 48 MET cc_start: 0.6778 (tpt) cc_final: 0.6399 (mmm) REVERT: E 92 PHE cc_start: 0.9214 (t80) cc_final: 0.8887 (t80) REVERT: R 38 ARG cc_start: 0.8002 (ptp-110) cc_final: 0.7589 (ptp-170) REVERT: R 280 ASP cc_start: 0.8422 (t0) cc_final: 0.8055 (t0) REVERT: R 324 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7527 (p-80) REVERT: R 373 MET cc_start: 0.8832 (mtt) cc_final: 0.8592 (mtm) REVERT: R 390 GLU cc_start: 0.9316 (mp0) cc_final: 0.8986 (mp0) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 0.0609 time to fit residues: 5.8877 Evaluate side-chains 74 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 324 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 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 = 0.103232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067371 restraints weight = 10163.697| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.75 r_work: 0.2936 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4060 Z= 0.122 Angle : 0.536 8.596 5563 Z= 0.283 Chirality : 0.038 0.201 646 Planarity : 0.003 0.030 690 Dihedral : 4.298 22.521 564 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.25 % Allowed : 15.17 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.58 (0.39), residues: 522 helix: 2.72 (0.27), residues: 372 sheet: 2.70 (1.47), residues: 12 loop : -1.39 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 112 TYR 0.010 0.001 TYR A 29 PHE 0.012 0.001 PHE E 92 TRP 0.019 0.001 TRP E 84 HIS 0.011 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4054) covalent geometry : angle 0.53551 ( 5551) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.57012 ( 12) hydrogen bonds : bond 0.04097 ( 284) hydrogen bonds : angle 3.58263 ( 843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9466 (mmm) cc_final: 0.9186 (mmm) REVERT: A 29 TYR cc_start: 0.9085 (m-80) cc_final: 0.8663 (m-80) REVERT: E 48 MET cc_start: 0.6852 (tpt) cc_final: 0.6437 (mmm) REVERT: E 84 TRP cc_start: 0.9425 (p-90) cc_final: 0.8946 (p-90) REVERT: E 92 PHE cc_start: 0.9246 (t80) cc_final: 0.8949 (t80) REVERT: R 38 ARG cc_start: 0.8057 (ptp-110) cc_final: 0.7675 (ptp-110) REVERT: R 99 GLU cc_start: 0.8418 (tp30) cc_final: 0.8020 (tm-30) REVERT: R 280 ASP cc_start: 0.8460 (t0) cc_final: 0.8099 (t0) REVERT: R 390 GLU cc_start: 0.9319 (mp0) cc_final: 0.8995 (mp0) outliers start: 8 outliers final: 6 residues processed: 77 average time/residue: 0.0545 time to fit residues: 5.3758 Evaluate side-chains 76 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.102423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066436 restraints weight = 10256.886| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.75 r_work: 0.2902 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4060 Z= 0.129 Angle : 0.550 9.313 5563 Z= 0.289 Chirality : 0.038 0.203 646 Planarity : 0.003 0.029 690 Dihedral : 4.227 22.654 564 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.53 % Allowed : 15.45 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.65 (0.39), residues: 522 helix: 2.82 (0.27), residues: 369 sheet: 2.79 (1.52), residues: 12 loop : -1.43 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.008 0.001 TYR A 29 PHE 0.012 0.001 PHE E 92 TRP 0.016 0.001 TRP E 59 HIS 0.013 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4054) covalent geometry : angle 0.54912 ( 5551) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.75861 ( 12) hydrogen bonds : bond 0.04206 ( 284) hydrogen bonds : angle 3.61129 ( 843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.9109 (m-80) cc_final: 0.8687 (m-80) REVERT: E 48 MET cc_start: 0.6974 (tpt) cc_final: 0.6562 (mmm) REVERT: E 84 TRP cc_start: 0.9437 (p-90) cc_final: 0.8914 (p-90) REVERT: R 38 ARG cc_start: 0.8097 (ptp-110) cc_final: 0.7745 (ptp-110) REVERT: R 99 GLU cc_start: 0.8508 (tp30) cc_final: 0.8108 (tm-30) REVERT: R 390 GLU cc_start: 0.9351 (mp0) cc_final: 0.9022 (mp0) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.0456 time to fit residues: 4.1301 Evaluate side-chains 74 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 20 HIS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.103259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067200 restraints weight = 10315.731| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.75 r_work: 0.2917 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4060 Z= 0.117 Angle : 0.566 10.431 5563 Z= 0.295 Chirality : 0.038 0.195 646 Planarity : 0.003 0.030 690 Dihedral : 4.188 22.630 564 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.09 % Allowed : 15.73 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.47 (0.39), residues: 522 helix: 2.65 (0.27), residues: 371 sheet: 2.82 (1.52), residues: 12 loop : -1.46 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.006 0.001 TYR A 29 PHE 0.011 0.001 PHE A 37 TRP 0.017 0.001 TRP E 59 HIS 0.011 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 4054) covalent geometry : angle 0.56553 ( 5551) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.56717 ( 12) hydrogen bonds : bond 0.04098 ( 284) hydrogen bonds : angle 3.59464 ( 843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9494 (mmm) cc_final: 0.9225 (mmm) REVERT: A 29 TYR cc_start: 0.9113 (m-80) cc_final: 0.8705 (m-80) REVERT: A 36 TYR cc_start: 0.8081 (m-80) cc_final: 0.7829 (m-80) REVERT: E 48 MET cc_start: 0.6997 (tpt) cc_final: 0.6581 (mmm) REVERT: E 84 TRP cc_start: 0.9419 (p-90) cc_final: 0.8916 (p-90) REVERT: R 38 ARG cc_start: 0.8114 (ptp-110) cc_final: 0.7748 (ptp-110) REVERT: R 99 GLU cc_start: 0.8599 (tp30) cc_final: 0.8254 (tm-30) REVERT: R 280 ASP cc_start: 0.8476 (t0) cc_final: 0.8112 (t0) REVERT: R 390 GLU cc_start: 0.9351 (mp0) cc_final: 0.9020 (mp0) outliers start: 11 outliers final: 9 residues processed: 74 average time/residue: 0.0540 time to fit residues: 5.1709 Evaluate side-chains 77 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.0270 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.102266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066418 restraints weight = 10176.258| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.73 r_work: 0.2904 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4060 Z= 0.128 Angle : 0.580 10.433 5563 Z= 0.301 Chirality : 0.038 0.201 646 Planarity : 0.003 0.029 690 Dihedral : 4.163 22.613 564 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.53 % Allowed : 16.01 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.58 (0.39), residues: 522 helix: 2.73 (0.28), residues: 370 sheet: 2.88 (1.53), residues: 12 loop : -1.39 (0.55), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 112 TYR 0.006 0.001 TYR R 365 PHE 0.018 0.001 PHE E 92 TRP 0.021 0.001 TRP E 59 HIS 0.006 0.001 HIS E 75 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4054) covalent geometry : angle 0.57970 ( 5551) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.59454 ( 12) hydrogen bonds : bond 0.04195 ( 284) hydrogen bonds : angle 3.70418 ( 843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9482 (mmm) cc_final: 0.9027 (mmm) REVERT: A 29 TYR cc_start: 0.9134 (m-80) cc_final: 0.8692 (m-80) REVERT: A 35 GLU cc_start: 0.9434 (tp30) cc_final: 0.9233 (tp30) REVERT: E 48 MET cc_start: 0.7053 (tpt) cc_final: 0.6651 (mmm) REVERT: E 84 TRP cc_start: 0.9427 (p-90) cc_final: 0.8952 (p-90) REVERT: E 113 ASP cc_start: 0.9230 (m-30) cc_final: 0.9002 (m-30) REVERT: R 38 ARG cc_start: 0.8214 (ptp-110) cc_final: 0.7829 (ptp-110) REVERT: R 99 GLU cc_start: 0.8674 (tp30) cc_final: 0.8335 (tm-30) REVERT: R 280 ASP cc_start: 0.8539 (t0) cc_final: 0.8185 (t0) REVERT: R 348 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8119 (mm-30) REVERT: R 390 GLU cc_start: 0.9347 (mp0) cc_final: 0.9014 (mp0) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.0469 time to fit residues: 4.3271 Evaluate side-chains 76 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.103854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067891 restraints weight = 10222.294| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.73 r_work: 0.2937 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4060 Z= 0.111 Angle : 0.570 10.814 5563 Z= 0.296 Chirality : 0.038 0.201 646 Planarity : 0.003 0.031 690 Dihedral : 4.113 22.405 564 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.25 % Allowed : 16.29 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.59 (0.39), residues: 522 helix: 2.80 (0.28), residues: 370 sheet: 2.17 (1.44), residues: 14 loop : -1.56 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 112 TYR 0.007 0.001 TYR R 365 PHE 0.013 0.001 PHE A 37 TRP 0.023 0.001 TRP E 59 HIS 0.004 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4054) covalent geometry : angle 0.57047 ( 5551) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.51271 ( 12) hydrogen bonds : bond 0.03884 ( 284) hydrogen bonds : angle 3.60696 ( 843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9462 (mmm) cc_final: 0.8910 (mmm) REVERT: A 29 TYR cc_start: 0.9116 (m-80) cc_final: 0.8680 (m-80) REVERT: E 84 TRP cc_start: 0.9456 (p-90) cc_final: 0.8976 (p-90) REVERT: R 38 ARG cc_start: 0.8247 (ptp-110) cc_final: 0.7943 (ptp-110) REVERT: R 99 GLU cc_start: 0.8679 (tp30) cc_final: 0.8414 (tm-30) REVERT: R 280 ASP cc_start: 0.8549 (t0) cc_final: 0.8214 (t0) REVERT: R 390 GLU cc_start: 0.9356 (mp0) cc_final: 0.9023 (mp0) outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.0556 time to fit residues: 5.2414 Evaluate side-chains 71 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067873 restraints weight = 10030.770| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.67 r_work: 0.2940 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4060 Z= 0.117 Angle : 0.614 11.768 5563 Z= 0.314 Chirality : 0.039 0.210 646 Planarity : 0.003 0.029 690 Dihedral : 4.054 22.086 564 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.12 % Allowed : 17.98 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.55 (0.39), residues: 522 helix: 2.76 (0.28), residues: 370 sheet: 2.14 (1.46), residues: 14 loop : -1.58 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 112 TYR 0.028 0.001 TYR R 91 PHE 0.017 0.001 PHE E 92 TRP 0.024 0.001 TRP E 59 HIS 0.003 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4054) covalent geometry : angle 0.61447 ( 5551) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.48770 ( 12) hydrogen bonds : bond 0.03843 ( 284) hydrogen bonds : angle 3.58608 ( 843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.9483 (mmm) cc_final: 0.9070 (mmm) REVERT: A 29 TYR cc_start: 0.9121 (m-80) cc_final: 0.8677 (m-80) REVERT: E 84 TRP cc_start: 0.9430 (p-90) cc_final: 0.9183 (p-90) REVERT: R 38 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.8028 (ptp-110) REVERT: R 99 GLU cc_start: 0.8681 (tp30) cc_final: 0.8426 (tm-30) REVERT: R 280 ASP cc_start: 0.8534 (t0) cc_final: 0.8203 (t0) REVERT: R 390 GLU cc_start: 0.9356 (mp0) cc_final: 0.9018 (mp0) outliers start: 4 outliers final: 4 residues processed: 72 average time/residue: 0.0578 time to fit residues: 5.2697 Evaluate side-chains 72 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 384 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 0.0980 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 overall best weight: 0.4520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.104839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068781 restraints weight = 10324.892| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.80 r_work: 0.2960 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4060 Z= 0.116 Angle : 0.622 11.656 5563 Z= 0.317 Chirality : 0.039 0.209 646 Planarity : 0.003 0.030 690 Dihedral : 4.148 21.904 564 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.69 % Allowed : 18.54 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.41 (0.39), residues: 522 helix: 2.69 (0.27), residues: 370 sheet: 2.15 (1.44), residues: 14 loop : -1.73 (0.54), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 112 TYR 0.035 0.001 TYR A 36 PHE 0.012 0.001 PHE A 37 TRP 0.024 0.001 TRP E 59 HIS 0.003 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4054) covalent geometry : angle 0.62137 ( 5551) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.85803 ( 12) hydrogen bonds : bond 0.03642 ( 284) hydrogen bonds : angle 3.56404 ( 843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 958.69 seconds wall clock time: 17 minutes 4.10 seconds (1024.10 seconds total)