Starting phenix.real_space_refine on Sat Aug 23 05:39:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cv9_7637/08_2025/6cv9_7637.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cv9_7637/08_2025/6cv9_7637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cv9_7637/08_2025/6cv9_7637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cv9_7637/08_2025/6cv9_7637.map" model { file = "/net/cci-nas-00/data/ceres_data/6cv9_7637/08_2025/6cv9_7637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cv9_7637/08_2025/6cv9_7637.cif" } resolution = 3.8 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= 0.005 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 56 5.16 5 C 6272 2.51 5 N 1740 2.21 5 O 1964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10032 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2508 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: B, C, D Time building chain proxies: 2.13, per 1000 atoms: 0.21 Number of scatterers: 10032 At special positions: 0 Unit cell: (114.21, 114.21, 107.16, 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 56 16.00 O 1964 8.00 N 1740 7.00 C 6272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 374.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 70.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.826A pdb=" N ALA A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.750A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.649A pdb=" N SER A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.604A pdb=" N LEU A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 874 Processing helix chain 'A' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.827A pdb=" N ALA B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.751A pdb=" N GLU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.648A pdb=" N SER B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 removed outlier: 3.605A pdb=" N LEU B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 874 Processing helix chain 'B' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU B 883 " --> pdb=" O ASN B 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 108 Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.827A pdb=" N ALA C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 226 through 237 removed outlier: 3.751A pdb=" N GLU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 removed outlier: 3.648A pdb=" N SER C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 337 removed outlier: 3.605A pdb=" N LEU C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 874 Processing helix chain 'C' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU C 883 " --> pdb=" O ASN C 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.827A pdb=" N ALA D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 219 through 225 Processing helix chain 'D' and resid 226 through 237 removed outlier: 3.751A pdb=" N GLU D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.648A pdb=" N SER D 258 " --> pdb=" O CYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Proline residue: D 292 - end of helix Processing helix chain 'D' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 337 removed outlier: 3.605A pdb=" N LEU D 332 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 874 Processing helix chain 'D' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU D 883 " --> pdb=" O ASN D 879 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1752 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: 1.36 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2997 1.33 - 1.45: 1391 1.45 - 1.57: 5708 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10176 Sorted by residual: bond pdb=" N LEU B 238 " pdb=" CA LEU B 238 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.28e-02 6.10e+03 4.15e+00 bond pdb=" N LEU D 238 " pdb=" CA LEU D 238 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.28e-02 6.10e+03 4.15e+00 bond pdb=" N LEU C 238 " pdb=" CA LEU C 238 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.28e-02 6.10e+03 4.15e+00 bond pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 1.456 1.431 0.026 1.28e-02 6.10e+03 4.01e+00 bond pdb=" CB PHE C 266 " pdb=" CG PHE C 266 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.65e+00 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12676 1.62 - 3.24: 792 3.24 - 4.86: 147 4.86 - 6.48: 61 6.48 - 8.10: 28 Bond angle restraints: 13704 Sorted by residual: angle pdb=" N LEU B 238 " pdb=" CA LEU B 238 " pdb=" C LEU B 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.53e+01 angle pdb=" N LEU C 238 " pdb=" CA LEU C 238 " pdb=" C LEU C 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.53e+01 angle pdb=" N LEU D 238 " pdb=" CA LEU D 238 " pdb=" C LEU D 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.53e+01 angle pdb=" N LEU A 238 " pdb=" CA LEU A 238 " pdb=" C LEU A 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.52e+01 angle pdb=" C ASN A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta sigma weight residual 120.33 124.29 -3.96 8.00e-01 1.56e+00 2.45e+01 ... (remaining 13699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 5991 14.33 - 28.66: 273 28.66 - 42.99: 60 42.99 - 57.32: 4 57.32 - 71.65: 4 Dihedral angle restraints: 6332 sinusoidal: 2584 harmonic: 3748 Sorted by residual: dihedral pdb=" CA ASP A 204 " pdb=" C ASP A 204 " pdb=" N PHE A 205 " pdb=" CA PHE A 205 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP D 204 " pdb=" C ASP D 204 " pdb=" N PHE D 205 " pdb=" CA PHE D 205 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP B 204 " pdb=" C ASP B 204 " pdb=" N PHE B 205 " pdb=" CA PHE B 205 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 6329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 914 0.042 - 0.083: 453 0.083 - 0.124: 137 0.124 - 0.165: 20 0.165 - 0.206: 16 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE C 273 " pdb=" N ILE C 273 " pdb=" C ILE C 273 " pdb=" CB ILE C 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1537 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 143 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLU D 143 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU D 143 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS D 144 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 143 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLU C 143 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU C 143 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS C 144 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 143 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLU B 143 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU B 143 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS B 144 " -0.012 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3095 2.83 - 3.35: 9834 3.35 - 3.87: 15792 3.87 - 4.38: 17920 4.38 - 4.90: 29817 Nonbonded interactions: 76458 Sorted by model distance: nonbonded pdb=" OE1 GLU A 885 " pdb=" NZ LYS B 887 " model vdw 2.316 3.120 nonbonded pdb=" O GLU A 899 " pdb=" OG SER A 902 " model vdw 2.333 3.040 nonbonded pdb=" O GLU D 899 " pdb=" OG SER D 902 " model vdw 2.333 3.040 nonbonded pdb=" O GLU C 899 " pdb=" OG SER C 902 " model vdw 2.333 3.040 nonbonded pdb=" O GLU B 899 " pdb=" OG SER B 902 " model vdw 2.333 3.040 ... (remaining 76453 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.006 0.079 10176 Z= 0.280 Angle : 0.998 8.098 13704 Z= 0.572 Chirality : 0.053 0.206 1540 Planarity : 0.006 0.034 1792 Dihedral : 9.512 71.650 3892 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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 aren not related in a simple way. whole: -3.93 (0.18), residues: 1248 helix: -1.85 (0.14), residues: 848 sheet: None (None), residues: 0 loop : -4.11 (0.23), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 174 TYR 0.035 0.003 TYR A 317 PHE 0.030 0.003 PHE D 313 HIS 0.004 0.001 HIS D 227 Details of bonding type rmsd covalent geometry : bond 0.00618 (10176) covalent geometry : angle 0.99827 (13704) hydrogen bonds : bond 0.12713 ( 584) hydrogen bonds : angle 6.08644 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.330 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: A 99 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8031 (pt0) REVERT: A 266 PHE cc_start: 0.8359 (t80) cc_final: 0.8101 (t80) REVERT: A 267 SER cc_start: 0.8503 (t) cc_final: 0.8247 (p) REVERT: B 128 VAL cc_start: 0.7412 (t) cc_final: 0.7061 (p) REVERT: B 273 ILE cc_start: 0.7913 (mm) cc_final: 0.7535 (mm) REVERT: B 287 LEU cc_start: 0.8958 (mt) cc_final: 0.8060 (mt) REVERT: B 306 LEU cc_start: 0.9265 (mt) cc_final: 0.8613 (mm) REVERT: B 877 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6356 (mt-10) REVERT: C 273 ILE cc_start: 0.7913 (mm) cc_final: 0.7579 (mm) REVERT: C 287 LEU cc_start: 0.9070 (mt) cc_final: 0.8101 (mt) REVERT: C 306 LEU cc_start: 0.9228 (mt) cc_final: 0.8587 (mm) REVERT: D 128 VAL cc_start: 0.7847 (t) cc_final: 0.7489 (p) REVERT: D 273 ILE cc_start: 0.7999 (mm) cc_final: 0.7698 (mm) REVERT: D 287 LEU cc_start: 0.8995 (mt) cc_final: 0.8093 (mt) REVERT: D 306 LEU cc_start: 0.9234 (mt) cc_final: 0.8614 (mm) REVERT: D 901 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7564 (ttmt) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1318 time to fit residues: 79.3656 Evaluate side-chains 212 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 235 HIS A 308 ASN A 870 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS B 904 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.104045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087447 restraints weight = 31792.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089963 restraints weight = 18931.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091679 restraints weight = 13360.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.092744 restraints weight = 10497.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.093591 restraints weight = 8933.913| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10176 Z= 0.185 Angle : 0.789 7.839 13704 Z= 0.412 Chirality : 0.042 0.155 1540 Planarity : 0.004 0.034 1792 Dihedral : 6.186 23.687 1376 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.29 % Allowed : 13.37 % Favored : 84.34 % 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 aren not related in a simple way. whole: -1.74 (0.22), residues: 1248 helix: 0.00 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -3.79 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 100 TYR 0.024 0.002 TYR D 231 PHE 0.018 0.002 PHE D 251 HIS 0.004 0.001 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00425 (10176) covalent geometry : angle 0.78939 (13704) hydrogen bonds : bond 0.04268 ( 584) hydrogen bonds : angle 4.86135 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.411 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: A 149 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: A 277 LYS cc_start: 0.8429 (mmpt) cc_final: 0.7942 (mmpt) REVERT: A 285 LEU cc_start: 0.9307 (mm) cc_final: 0.8901 (pt) REVERT: A 288 SER cc_start: 0.8756 (p) cc_final: 0.8213 (p) REVERT: A 858 MET cc_start: 0.8741 (mmm) cc_final: 0.8430 (tpp) REVERT: A 911 LEU cc_start: 0.8593 (tt) cc_final: 0.8312 (mt) REVERT: B 128 VAL cc_start: 0.7252 (t) cc_final: 0.6918 (p) REVERT: B 876 ASP cc_start: 0.8341 (p0) cc_final: 0.8127 (p0) REVERT: B 877 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6986 (mt-10) REVERT: B 911 LEU cc_start: 0.8265 (tt) cc_final: 0.8053 (mm) REVERT: C 298 GLU cc_start: 0.7919 (tt0) cc_final: 0.7634 (tt0) REVERT: D 128 VAL cc_start: 0.7581 (t) cc_final: 0.7293 (p) REVERT: D 149 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7553 (tm-30) outliers start: 25 outliers final: 13 residues processed: 252 average time/residue: 0.0792 time to fit residues: 28.4139 Evaluate side-chains 201 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 312 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 0.0570 chunk 10 optimal weight: 0.0670 chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS A 904 ASN B 126 ASN B 144 HIS C 126 ASN C 144 HIS C 217 HIS ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 217 HIS D 227 HIS ** D 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.103586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086650 restraints weight = 31992.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089264 restraints weight = 19173.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090931 restraints weight = 13498.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092138 restraints weight = 10594.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.092861 restraints weight = 8943.582| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10176 Z= 0.148 Angle : 0.724 8.189 13704 Z= 0.380 Chirality : 0.041 0.146 1540 Planarity : 0.004 0.031 1792 Dihedral : 5.847 21.236 1376 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.66 % Allowed : 15.75 % Favored : 81.59 % 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 aren not related in a simple way. whole: -0.91 (0.23), residues: 1248 helix: 0.68 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -3.70 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 894 TYR 0.025 0.002 TYR D 231 PHE 0.016 0.001 PHE B 251 HIS 0.005 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00329 (10176) covalent geometry : angle 0.72368 (13704) hydrogen bonds : bond 0.03874 ( 584) hydrogen bonds : angle 4.55686 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 0.309 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: A 149 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 285 LEU cc_start: 0.9220 (mm) cc_final: 0.8855 (pt) REVERT: A 319 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8439 (tttt) REVERT: A 858 MET cc_start: 0.8605 (mmm) cc_final: 0.8275 (tpp) REVERT: A 874 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8132 (tm-30) REVERT: A 911 LEU cc_start: 0.8733 (tt) cc_final: 0.8426 (mt) REVERT: B 277 LYS cc_start: 0.8280 (mmtt) cc_final: 0.8022 (mmtt) REVERT: B 876 ASP cc_start: 0.8421 (p0) cc_final: 0.8179 (p0) REVERT: B 911 LEU cc_start: 0.8259 (tt) cc_final: 0.7778 (mt) REVERT: C 858 MET cc_start: 0.8840 (mmm) cc_final: 0.8618 (mmm) REVERT: C 877 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6567 (mt-10) REVERT: C 911 LEU cc_start: 0.8393 (tt) cc_final: 0.8037 (mt) REVERT: D 128 VAL cc_start: 0.7696 (t) cc_final: 0.7414 (p) REVERT: D 149 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: D 252 CYS cc_start: 0.9265 (t) cc_final: 0.8983 (t) outliers start: 29 outliers final: 18 residues processed: 198 average time/residue: 0.0696 time to fit residues: 19.8606 Evaluate side-chains 182 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 227 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 227 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.102309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085473 restraints weight = 32114.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.088021 restraints weight = 19017.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089690 restraints weight = 13334.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.090832 restraints weight = 10456.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.091586 restraints weight = 8830.381| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10176 Z= 0.145 Angle : 0.679 7.219 13704 Z= 0.354 Chirality : 0.040 0.142 1540 Planarity : 0.003 0.033 1792 Dihedral : 5.635 25.538 1376 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.47 % Allowed : 17.22 % Favored : 80.31 % 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 aren not related in a simple way. whole: -0.40 (0.24), residues: 1248 helix: 1.13 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -3.72 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 894 TYR 0.027 0.002 TYR A 231 PHE 0.019 0.001 PHE B 251 HIS 0.005 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00329 (10176) covalent geometry : angle 0.67863 (13704) hydrogen bonds : bond 0.03656 ( 584) hydrogen bonds : angle 4.43784 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: A 285 LEU cc_start: 0.9199 (mm) cc_final: 0.8635 (pt) REVERT: A 306 LEU cc_start: 0.8707 (pt) cc_final: 0.7942 (pt) REVERT: A 319 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8489 (tmtt) REVERT: A 858 MET cc_start: 0.8534 (mmm) cc_final: 0.8190 (tpp) REVERT: A 880 GLU cc_start: 0.7007 (mp0) cc_final: 0.5684 (mp0) REVERT: A 911 LEU cc_start: 0.8739 (tt) cc_final: 0.8352 (mt) REVERT: B 201 GLN cc_start: 0.6131 (pm20) cc_final: 0.5671 (pm20) REVERT: B 277 LYS cc_start: 0.8357 (mmtt) cc_final: 0.8050 (mmtt) REVERT: B 858 MET cc_start: 0.8953 (mmm) cc_final: 0.8728 (mmm) REVERT: B 911 LEU cc_start: 0.8186 (tt) cc_final: 0.7801 (mt) REVERT: C 128 VAL cc_start: 0.7721 (t) cc_final: 0.7505 (p) REVERT: C 149 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 201 GLN cc_start: 0.5794 (pm20) cc_final: 0.5508 (pm20) REVERT: C 858 MET cc_start: 0.8822 (mmm) cc_final: 0.8616 (mmm) REVERT: C 911 LEU cc_start: 0.8296 (tt) cc_final: 0.7965 (mt) REVERT: D 149 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: D 273 ILE cc_start: 0.8093 (mm) cc_final: 0.7518 (mm) REVERT: D 285 LEU cc_start: 0.9295 (mm) cc_final: 0.8878 (pt) outliers start: 27 outliers final: 18 residues processed: 186 average time/residue: 0.0772 time to fit residues: 20.4389 Evaluate side-chains 172 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN C 217 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.100679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083885 restraints weight = 32121.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086393 restraints weight = 19056.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.088050 restraints weight = 13396.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089154 restraints weight = 10533.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089868 restraints weight = 8933.378| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10176 Z= 0.164 Angle : 0.687 7.088 13704 Z= 0.360 Chirality : 0.040 0.140 1540 Planarity : 0.004 0.051 1792 Dihedral : 5.556 25.980 1376 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.20 % Allowed : 19.41 % Favored : 78.39 % 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 aren not related in a simple way. whole: -0.22 (0.25), residues: 1248 helix: 1.34 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -3.80 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 894 TYR 0.023 0.002 TYR A 231 PHE 0.020 0.001 PHE D 251 HIS 0.005 0.001 HIS C 263 Details of bonding type rmsd covalent geometry : bond 0.00371 (10176) covalent geometry : angle 0.68716 (13704) hydrogen bonds : bond 0.03678 ( 584) hydrogen bonds : angle 4.44798 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.257 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: A 153 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8780 (mtpp) REVERT: A 215 PHE cc_start: 0.7831 (t80) cc_final: 0.7476 (t80) REVERT: A 285 LEU cc_start: 0.9219 (mm) cc_final: 0.8893 (pt) REVERT: A 312 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7692 (mm-30) REVERT: A 858 MET cc_start: 0.8590 (mmm) cc_final: 0.8227 (tpp) REVERT: A 911 LEU cc_start: 0.8659 (tt) cc_final: 0.8428 (mt) REVERT: B 880 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7543 (mt-10) REVERT: B 911 LEU cc_start: 0.8272 (tt) cc_final: 0.7887 (mt) REVERT: C 128 VAL cc_start: 0.7969 (t) cc_final: 0.7713 (p) REVERT: C 285 LEU cc_start: 0.9301 (mm) cc_final: 0.8913 (pt) REVERT: C 858 MET cc_start: 0.8812 (mmm) cc_final: 0.8589 (mmm) REVERT: C 877 GLU cc_start: 0.6275 (mt-10) cc_final: 0.5850 (mt-10) REVERT: C 911 LEU cc_start: 0.8300 (tt) cc_final: 0.7930 (mt) REVERT: D 149 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: D 285 LEU cc_start: 0.9326 (mm) cc_final: 0.8911 (pt) REVERT: D 900 GLU cc_start: 0.7223 (tp30) cc_final: 0.6749 (tp30) outliers start: 24 outliers final: 14 residues processed: 186 average time/residue: 0.0743 time to fit residues: 20.0147 Evaluate side-chains 166 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 0.0980 chunk 40 optimal weight: 0.0870 chunk 83 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 HIS D 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.102347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085497 restraints weight = 31821.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088064 restraints weight = 18822.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089777 restraints weight = 13185.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090952 restraints weight = 10317.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091747 restraints weight = 8672.898| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10176 Z= 0.129 Angle : 0.677 11.439 13704 Z= 0.349 Chirality : 0.040 0.150 1540 Planarity : 0.003 0.043 1792 Dihedral : 5.489 25.807 1376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.38 % Allowed : 20.15 % Favored : 77.47 % 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 aren not related in a simple way. whole: 0.01 (0.25), residues: 1248 helix: 1.56 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.77 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 894 TYR 0.024 0.002 TYR A 231 PHE 0.014 0.001 PHE D 251 HIS 0.004 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00285 (10176) covalent geometry : angle 0.67663 (13704) hydrogen bonds : bond 0.03507 ( 584) hydrogen bonds : angle 4.27514 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.265 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: A 118 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8036 (pt0) REVERT: A 153 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8813 (mtpp) REVERT: A 285 LEU cc_start: 0.9122 (mm) cc_final: 0.8827 (pt) REVERT: A 312 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 858 MET cc_start: 0.8545 (mmm) cc_final: 0.8212 (tpp) REVERT: A 911 LEU cc_start: 0.8655 (tt) cc_final: 0.8237 (mt) REVERT: B 149 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 201 GLN cc_start: 0.6215 (pm20) cc_final: 0.5926 (pm20) REVERT: B 880 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7385 (mm-30) REVERT: B 911 LEU cc_start: 0.8288 (tt) cc_final: 0.7892 (mt) REVERT: C 285 LEU cc_start: 0.9309 (mm) cc_final: 0.8892 (pt) REVERT: C 858 MET cc_start: 0.8773 (mmm) cc_final: 0.8559 (mmm) REVERT: C 877 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6489 (mt-10) REVERT: C 880 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7460 (mt-10) REVERT: C 911 LEU cc_start: 0.8152 (tt) cc_final: 0.7870 (mt) REVERT: D 149 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: D 285 LEU cc_start: 0.9319 (mm) cc_final: 0.8897 (pt) outliers start: 26 outliers final: 10 residues processed: 180 average time/residue: 0.0737 time to fit residues: 19.5795 Evaluate side-chains 160 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS A 201 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.100137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083647 restraints weight = 31957.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.086119 restraints weight = 18922.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087795 restraints weight = 13293.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088814 restraints weight = 10413.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089635 restraints weight = 8861.311| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10176 Z= 0.158 Angle : 0.679 9.345 13704 Z= 0.353 Chirality : 0.041 0.160 1540 Planarity : 0.003 0.043 1792 Dihedral : 5.354 25.539 1376 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.74 % Allowed : 20.70 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.25), residues: 1248 helix: 1.63 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.74 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.017 0.002 TYR A 231 PHE 0.011 0.001 PHE D 251 HIS 0.004 0.001 HIS D 263 Details of bonding type rmsd covalent geometry : bond 0.00362 (10176) covalent geometry : angle 0.67872 (13704) hydrogen bonds : bond 0.03586 ( 584) hydrogen bonds : angle 4.38667 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8805 (mtpp) REVERT: A 215 PHE cc_start: 0.7927 (t80) cc_final: 0.7563 (t80) REVERT: A 858 MET cc_start: 0.8607 (mmm) cc_final: 0.8232 (tpp) REVERT: A 911 LEU cc_start: 0.8669 (tt) cc_final: 0.8432 (mt) REVERT: B 880 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7422 (mm-30) REVERT: B 911 LEU cc_start: 0.8248 (tt) cc_final: 0.7776 (mt) REVERT: C 285 LEU cc_start: 0.9330 (mm) cc_final: 0.8938 (pt) REVERT: C 312 GLU cc_start: 0.7526 (mp0) cc_final: 0.7146 (mp0) REVERT: C 858 MET cc_start: 0.8818 (mmm) cc_final: 0.8586 (mmm) REVERT: C 877 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6047 (mt-10) REVERT: C 911 LEU cc_start: 0.8217 (tt) cc_final: 0.7901 (mt) REVERT: D 149 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: D 285 LEU cc_start: 0.9329 (mm) cc_final: 0.8827 (pt) REVERT: D 320 LEU cc_start: 0.8202 (mt) cc_final: 0.7902 (mt) REVERT: D 880 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7375 (mt-10) REVERT: D 900 GLU cc_start: 0.7838 (tt0) cc_final: 0.7595 (tt0) outliers start: 19 outliers final: 12 residues processed: 171 average time/residue: 0.0727 time to fit residues: 18.4106 Evaluate side-chains 162 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 72 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 52 optimal weight: 0.0020 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085413 restraints weight = 31387.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087961 restraints weight = 18368.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089666 restraints weight = 12715.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090805 restraints weight = 9851.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091596 restraints weight = 8214.734| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10176 Z= 0.137 Angle : 0.681 9.428 13704 Z= 0.350 Chirality : 0.040 0.181 1540 Planarity : 0.003 0.040 1792 Dihedral : 5.326 25.775 1376 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.65 % Allowed : 21.52 % Favored : 76.83 % 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 aren not related in a simple way. whole: 0.27 (0.25), residues: 1248 helix: 1.81 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -3.75 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 894 TYR 0.022 0.002 TYR A 231 PHE 0.011 0.001 PHE D 251 HIS 0.004 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00306 (10176) covalent geometry : angle 0.68078 (13704) hydrogen bonds : bond 0.03413 ( 584) hydrogen bonds : angle 4.22538 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9015 (mmmt) cc_final: 0.8770 (mtpp) REVERT: A 858 MET cc_start: 0.8590 (mmm) cc_final: 0.8249 (tpp) REVERT: A 911 LEU cc_start: 0.8656 (tt) cc_final: 0.8335 (mt) REVERT: B 911 LEU cc_start: 0.8238 (tt) cc_final: 0.7865 (mt) REVERT: C 285 LEU cc_start: 0.9343 (mm) cc_final: 0.8903 (pt) REVERT: C 858 MET cc_start: 0.8821 (mmm) cc_final: 0.8615 (mmm) REVERT: C 872 ASP cc_start: 0.8760 (t0) cc_final: 0.8500 (t70) REVERT: C 877 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5875 (mt-10) REVERT: C 911 LEU cc_start: 0.8182 (tt) cc_final: 0.7949 (mt) REVERT: D 128 VAL cc_start: 0.8140 (t) cc_final: 0.7931 (p) REVERT: D 149 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: D 285 LEU cc_start: 0.9149 (mm) cc_final: 0.8606 (pt) REVERT: D 872 ASP cc_start: 0.8802 (t0) cc_final: 0.8469 (t70) REVERT: D 880 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7509 (mt-10) outliers start: 18 outliers final: 10 residues processed: 171 average time/residue: 0.0771 time to fit residues: 19.4808 Evaluate side-chains 162 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 319 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 0.0020 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084660 restraints weight = 31867.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087164 restraints weight = 18808.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088872 restraints weight = 13152.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089995 restraints weight = 10255.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090712 restraints weight = 8632.916| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10176 Z= 0.144 Angle : 0.700 12.116 13704 Z= 0.364 Chirality : 0.041 0.209 1540 Planarity : 0.003 0.038 1792 Dihedral : 5.202 25.516 1376 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.10 % Allowed : 22.07 % Favored : 76.83 % 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 aren not related in a simple way. whole: 0.26 (0.25), residues: 1248 helix: 1.79 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -3.72 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 894 TYR 0.023 0.002 TYR A 231 PHE 0.010 0.001 PHE D 251 HIS 0.004 0.001 HIS D 227 Details of bonding type rmsd covalent geometry : bond 0.00328 (10176) covalent geometry : angle 0.69971 (13704) hydrogen bonds : bond 0.03547 ( 584) hydrogen bonds : angle 4.29904 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8762 (mtpp) REVERT: A 858 MET cc_start: 0.8575 (mmm) cc_final: 0.8227 (tpp) REVERT: B 911 LEU cc_start: 0.8272 (tt) cc_final: 0.7902 (mt) REVERT: C 285 LEU cc_start: 0.9340 (mm) cc_final: 0.8929 (pt) REVERT: C 858 MET cc_start: 0.8803 (mmm) cc_final: 0.8589 (mmm) REVERT: C 872 ASP cc_start: 0.8753 (t0) cc_final: 0.8496 (t70) REVERT: C 880 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7240 (mm-30) REVERT: C 911 LEU cc_start: 0.8326 (tt) cc_final: 0.8019 (mt) REVERT: D 285 LEU cc_start: 0.9171 (mm) cc_final: 0.8619 (pt) REVERT: D 872 ASP cc_start: 0.8770 (t0) cc_final: 0.8511 (t70) REVERT: D 880 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7457 (mt-10) outliers start: 12 outliers final: 9 residues processed: 158 average time/residue: 0.0736 time to fit residues: 17.4137 Evaluate side-chains 154 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 74 optimal weight: 0.0870 chunk 111 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 44 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.101852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085609 restraints weight = 31507.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088157 restraints weight = 18821.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089880 restraints weight = 13155.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091018 restraints weight = 10233.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.091738 restraints weight = 8585.347| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10176 Z= 0.139 Angle : 0.710 11.950 13704 Z= 0.370 Chirality : 0.042 0.240 1540 Planarity : 0.004 0.078 1792 Dihedral : 5.156 25.373 1376 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.82 % Allowed : 22.34 % Favored : 76.83 % 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 aren not related in a simple way. whole: 0.25 (0.25), residues: 1248 helix: 1.76 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -3.66 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 318 TYR 0.019 0.002 TYR D 231 PHE 0.010 0.001 PHE D 251 HIS 0.005 0.001 HIS C 227 Details of bonding type rmsd covalent geometry : bond 0.00309 (10176) covalent geometry : angle 0.71049 (13704) hydrogen bonds : bond 0.03590 ( 584) hydrogen bonds : angle 4.37391 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8758 (mtpp) REVERT: A 177 GLU cc_start: 0.8116 (tp30) cc_final: 0.7913 (tp30) REVERT: A 858 MET cc_start: 0.8559 (mmm) cc_final: 0.8220 (tpp) REVERT: B 285 LEU cc_start: 0.9351 (mm) cc_final: 0.8937 (pt) REVERT: B 911 LEU cc_start: 0.8219 (tt) cc_final: 0.7951 (mt) REVERT: C 285 LEU cc_start: 0.9353 (mm) cc_final: 0.8951 (pt) REVERT: C 858 MET cc_start: 0.8787 (mmm) cc_final: 0.8581 (mmm) REVERT: C 872 ASP cc_start: 0.8739 (t0) cc_final: 0.8491 (t70) REVERT: C 880 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7296 (mm-30) REVERT: C 911 LEU cc_start: 0.8374 (tt) cc_final: 0.8024 (mt) REVERT: D 285 LEU cc_start: 0.9173 (mm) cc_final: 0.8563 (pt) REVERT: D 872 ASP cc_start: 0.8737 (t0) cc_final: 0.8496 (t70) REVERT: D 880 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7451 (mt-10) outliers start: 9 outliers final: 8 residues processed: 155 average time/residue: 0.0769 time to fit residues: 17.8331 Evaluate side-chains 152 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 chunk 107 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.0270 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.103360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086718 restraints weight = 31793.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089324 restraints weight = 19056.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.091046 restraints weight = 13379.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.092196 restraints weight = 10467.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.092968 restraints weight = 8810.969| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10176 Z= 0.136 Angle : 0.698 12.345 13704 Z= 0.362 Chirality : 0.041 0.173 1540 Planarity : 0.003 0.035 1792 Dihedral : 5.050 24.971 1376 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.92 % Allowed : 22.62 % Favored : 76.47 % 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 aren not related in a simple way. whole: 0.38 (0.25), residues: 1248 helix: 1.85 (0.19), residues: 852 sheet: None (None), residues: 0 loop : -3.62 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 318 TYR 0.023 0.002 TYR A 231 PHE 0.010 0.001 PHE D 251 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00300 (10176) covalent geometry : angle 0.69823 (13704) hydrogen bonds : bond 0.03427 ( 584) hydrogen bonds : angle 4.26297 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.19 seconds wall clock time: 24 minutes 47.71 seconds (1487.71 seconds total)