Starting phenix.real_space_refine on Mon Jul 28 05:02:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cv9_7637/07_2025/6cv9_7637.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cv9_7637/07_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_7637/07_2025/6cv9_7637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cv9_7637/07_2025/6cv9_7637.map" model { file = "/net/cci-nas-00/data/ceres_data/6cv9_7637/07_2025/6cv9_7637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cv9_7637/07_2025/6cv9_7637.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Restraints were copied for chains: C, B, D Time building chain proxies: 5.75, per 1000 atoms: 0.57 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: 3.81 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 0.97 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: 2.89 Time building geometry restraints manager: 4.75 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 32.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.001 HIS D 227 PHE 0.030 0.003 PHE D 313 TYR 0.035 0.003 TYR A 317 ARG 0.006 0.001 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.12713 ( 584) hydrogen bonds : angle 6.08644 ( 1752) covalent geometry : bond 0.00618 (10176) covalent geometry : angle 0.99827 (13704) *********************** 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 : 1.324 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 99 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8019 (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: 0.8246 (p) REVERT: B 128 VAL cc_start: 0.7412 (t) cc_final: 0.7055 (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: 0.8059 (mt) REVERT: B 306 LEU cc_start: 0.9265 (mt) cc_final: 0.8612 (mm) REVERT: B 877 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6353 (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: 0.8100 (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: 0.7487 (p) REVERT: D 273 ILE cc_start: 0.7999 (mm) cc_final: 0.7702 (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: 0.3022 time to fit residues: 180.4800 Evaluate side-chains 206 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.0170 chunk 63 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 855 GLN ** 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 D 308 ASN D 855 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.106316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089896 restraints weight = 31540.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.092490 restraints weight = 18727.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094244 restraints weight = 13102.402| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10176 Z= 0.161 Angle : 0.780 7.779 13704 Z= 0.406 Chirality : 0.041 0.123 1540 Planarity : 0.004 0.032 1792 Dihedral : 6.213 22.143 1376 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 1.92 % Allowed : 13.92 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1248 helix: -0.07 (0.17), residues: 848 sheet: None (None), residues: 0 loop : -3.77 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 248 PHE 0.018 0.002 PHE A 251 TYR 0.024 0.002 TYR D 231 ARG 0.008 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 584) hydrogen bonds : angle 4.75908 ( 1752) covalent geometry : bond 0.00365 (10176) covalent geometry : angle 0.78015 (13704) *********************** 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 262 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 1.305 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: 0.8166 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: A 277 LYS cc_start: 0.8359 (mmpt) cc_final: 0.7919 (mmpt) REVERT: A 285 LEU cc_start: 0.9307 (mm) cc_final: 0.8930 (pt) REVERT: A 288 SER cc_start: 0.8720 (p) cc_final: 0.8188 (p) REVERT: A 858 MET cc_start: 0.8687 (mmm) cc_final: 0.8412 (tpp) REVERT: A 872 ASP cc_start: 0.8754 (t0) cc_final: 0.8540 (t70) REVERT: A 911 LEU cc_start: 0.8590 (tt) cc_final: 0.8353 (mt) REVERT: B 128 VAL cc_start: 0.7159 (t) cc_final: 0.6895 (p) REVERT: B 876 ASP cc_start: 0.8305 (p0) cc_final: 0.8076 (p0) REVERT: B 877 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6637 (mt-10) REVERT: C 128 VAL cc_start: 0.7256 (t) cc_final: 0.6990 (p) REVERT: C 900 GLU cc_start: 0.7705 (tt0) cc_final: 0.7481 (tt0) REVERT: D 128 VAL cc_start: 0.7452 (t) cc_final: 0.7214 (p) outliers start: 21 outliers final: 11 residues processed: 254 average time/residue: 0.1999 time to fit residues: 72.2576 Evaluate side-chains 195 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 213 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 312 GLU 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 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 70 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 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 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 904 ASN B 126 ASN B 144 HIS B 855 GLN B 904 ASN C 126 ASN C 144 HIS C 217 HIS C 904 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.103622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.086632 restraints weight = 32038.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089199 restraints weight = 19185.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090874 restraints weight = 13533.807| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10176 Z= 0.164 Angle : 0.720 7.512 13704 Z= 0.379 Chirality : 0.041 0.187 1540 Planarity : 0.004 0.030 1792 Dihedral : 5.787 21.283 1376 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.56 % Allowed : 16.21 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1248 helix: 0.71 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -3.73 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 263 PHE 0.018 0.001 PHE B 251 TYR 0.019 0.002 TYR D 231 ARG 0.004 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 584) hydrogen bonds : angle 4.55954 ( 1752) covalent geometry : bond 0.00370 (10176) covalent geometry : angle 0.72022 (13704) *********************** 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 216 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.173 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: A 128 VAL cc_start: 0.8006 (t) cc_final: 0.7796 (p) REVERT: A 285 LEU cc_start: 0.9272 (mm) cc_final: 0.8874 (pt) REVERT: A 306 LEU cc_start: 0.8894 (mt) cc_final: 0.8683 (pt) REVERT: A 319 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8501 (tttt) REVERT: A 858 MET cc_start: 0.8634 (mmm) cc_final: 0.8275 (tpp) REVERT: A 911 LEU cc_start: 0.8941 (tt) cc_final: 0.8620 (mm) REVERT: B 252 CYS cc_start: 0.9262 (t) cc_final: 0.8955 (t) REVERT: B 876 ASP cc_start: 0.8363 (p0) cc_final: 0.8115 (p0) REVERT: C 128 VAL cc_start: 0.7553 (t) cc_final: 0.7297 (p) REVERT: C 274 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: C 858 MET cc_start: 0.8848 (mmm) cc_final: 0.8630 (mmm) REVERT: C 911 LEU cc_start: 0.8378 (tt) cc_final: 0.8138 (mt) REVERT: D 128 VAL cc_start: 0.7730 (t) cc_final: 0.7443 (p) REVERT: D 252 CYS cc_start: 0.9342 (t) cc_final: 0.9065 (t) REVERT: D 274 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8408 (m-40) REVERT: D 911 LEU cc_start: 0.8564 (tt) cc_final: 0.8341 (mm) outliers start: 28 outliers final: 15 residues processed: 201 average time/residue: 0.2036 time to fit residues: 58.3134 Evaluate side-chains 185 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain A residue 213 THR 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 312 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 274 ASN 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 42 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.101832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.085280 restraints weight = 31851.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087826 restraints weight = 18790.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089487 restraints weight = 13132.655| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5565 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= 0.149 Angle : 0.668 7.024 13704 Z= 0.353 Chirality : 0.040 0.141 1540 Planarity : 0.003 0.031 1792 Dihedral : 5.575 26.440 1376 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.47 % Allowed : 17.31 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1248 helix: 1.24 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.74 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 263 PHE 0.021 0.001 PHE C 251 TYR 0.023 0.002 TYR D 231 ARG 0.004 0.001 ARG C 894 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 584) hydrogen bonds : angle 4.39475 ( 1752) covalent geometry : bond 0.00338 (10176) covalent geometry : angle 0.66794 (13704) *********************** 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 212 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.211 Fit side-chains 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: 0.7826 (tm-30) REVERT: A 285 LEU cc_start: 0.9260 (mm) cc_final: 0.8744 (pt) REVERT: A 858 MET cc_start: 0.8514 (mmm) cc_final: 0.8169 (tpp) REVERT: B 201 GLN cc_start: 0.6132 (pm20) cc_final: 0.5761 (pm20) REVERT: B 858 MET cc_start: 0.8947 (mmm) cc_final: 0.8731 (mmm) REVERT: B 877 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6459 (mt-10) REVERT: B 880 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7564 (mt-10) REVERT: C 128 VAL cc_start: 0.7677 (t) cc_final: 0.7462 (p) REVERT: C 149 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 201 GLN cc_start: 0.5761 (pm20) cc_final: 0.5536 (pm20) REVERT: C 252 CYS cc_start: 0.8985 (t) cc_final: 0.8706 (t) REVERT: C 858 MET cc_start: 0.8779 (mmm) cc_final: 0.8568 (mmm) REVERT: D 128 VAL cc_start: 0.7876 (t) cc_final: 0.7622 (p) REVERT: D 285 LEU cc_start: 0.9286 (mm) cc_final: 0.8950 (pt) REVERT: D 312 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7563 (mp0) outliers start: 27 outliers final: 16 residues processed: 199 average time/residue: 0.2706 time to fit residues: 75.5887 Evaluate side-chains 167 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU 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 266 PHE 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 36 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 47 optimal weight: 0.0170 chunk 41 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 217 HIS ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 217 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.085272 restraints weight = 31618.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087813 restraints weight = 18642.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089500 restraints weight = 12982.445| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5825 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= 0.134 Angle : 0.655 6.802 13704 Z= 0.346 Chirality : 0.040 0.151 1540 Planarity : 0.004 0.049 1792 Dihedral : 5.535 25.577 1376 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.75 % Allowed : 18.41 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1248 helix: 1.25 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.85 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 263 PHE 0.020 0.001 PHE C 251 TYR 0.021 0.002 TYR B 231 ARG 0.003 0.001 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 584) hydrogen bonds : angle 4.34047 ( 1752) covalent geometry : bond 0.00300 (10176) covalent geometry : angle 0.65492 (13704) *********************** 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: 30 poor density : 164 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 153 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8585 (mtpp) REVERT: A 285 LEU cc_start: 0.9158 (mm) cc_final: 0.8684 (pt) REVERT: B 149 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7116 (tm-30) REVERT: B 201 GLN cc_start: 0.6127 (pm20) cc_final: 0.5927 (pm20) REVERT: B 877 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6576 (mt-10) REVERT: B 880 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 128 VAL cc_start: 0.7854 (t) cc_final: 0.7501 (p) REVERT: C 285 LEU cc_start: 0.9306 (mm) cc_final: 0.8885 (pt) REVERT: C 858 MET cc_start: 0.8748 (mmm) cc_final: 0.8529 (mmm) REVERT: C 900 GLU cc_start: 0.7705 (tt0) cc_final: 0.7165 (tt0) REVERT: D 128 VAL cc_start: 0.7904 (t) cc_final: 0.7672 (p) REVERT: D 285 LEU cc_start: 0.9327 (mm) cc_final: 0.8934 (pt) REVERT: D 312 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7321 (mp0) REVERT: D 900 GLU cc_start: 0.7052 (tp30) cc_final: 0.6621 (tp30) outliers start: 30 outliers final: 14 residues processed: 182 average time/residue: 0.3189 time to fit residues: 86.1312 Evaluate side-chains 167 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU 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 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 53 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.100706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084735 restraints weight = 31453.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.087240 restraints weight = 18394.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088903 restraints weight = 12765.316| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6117 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 : 0.660 8.268 13704 Z= 0.349 Chirality : 0.041 0.207 1540 Planarity : 0.004 0.046 1792 Dihedral : 5.419 26.819 1376 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.84 % Allowed : 19.23 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1248 helix: 1.44 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -3.84 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 263 PHE 0.011 0.001 PHE D 251 TYR 0.016 0.002 TYR C 231 ARG 0.003 0.001 ARG A 894 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 584) hydrogen bonds : angle 4.35840 ( 1752) covalent geometry : bond 0.00335 (10176) covalent geometry : angle 0.66022 (13704) *********************** 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 187 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: A 153 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8585 (mtpp) REVERT: A 285 LEU cc_start: 0.9249 (mm) cc_final: 0.8756 (pt) REVERT: B 877 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6590 (mt-10) REVERT: B 880 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 285 LEU cc_start: 0.9328 (mm) cc_final: 0.8877 (pt) REVERT: C 858 MET cc_start: 0.8810 (mmm) cc_final: 0.8595 (mmm) REVERT: C 872 ASP cc_start: 0.8722 (m-30) cc_final: 0.8494 (t0) REVERT: D 273 ILE cc_start: 0.8152 (mm) cc_final: 0.7629 (mp) REVERT: D 285 LEU cc_start: 0.9350 (mm) cc_final: 0.8939 (pt) REVERT: D 312 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7439 (mp0) REVERT: D 880 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7397 (mt-10) outliers start: 31 outliers final: 14 residues processed: 172 average time/residue: 0.2771 time to fit residues: 69.4991 Evaluate side-chains 161 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 885 GLU 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 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 904 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083519 restraints weight = 32140.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085988 restraints weight = 18896.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087636 restraints weight = 13212.618| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10176 Z= 0.160 Angle : 0.681 9.136 13704 Z= 0.359 Chirality : 0.041 0.161 1540 Planarity : 0.004 0.046 1792 Dihedral : 5.378 26.795 1376 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 1.65 % Allowed : 20.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1248 helix: 1.51 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -3.86 (0.25), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 263 PHE 0.011 0.001 PHE D 251 TYR 0.025 0.002 TYR A 231 ARG 0.006 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 584) hydrogen bonds : angle 4.34719 ( 1752) covalent geometry : bond 0.00370 (10176) covalent geometry : angle 0.68109 (13704) *********************** 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 169 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 153 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8537 (mtpp) REVERT: A 285 LEU cc_start: 0.9308 (mm) cc_final: 0.8794 (pt) REVERT: A 306 LEU cc_start: 0.8467 (pt) cc_final: 0.8267 (pt) REVERT: B 877 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6705 (mt-10) REVERT: B 880 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7520 (mm-30) REVERT: C 285 LEU cc_start: 0.9340 (mm) cc_final: 0.8935 (pt) REVERT: C 858 MET cc_start: 0.8822 (mmm) cc_final: 0.8616 (mmm) REVERT: C 872 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8531 (t0) REVERT: C 900 GLU cc_start: 0.7964 (tt0) cc_final: 0.7452 (tt0) REVERT: D 285 LEU cc_start: 0.9355 (mm) cc_final: 0.8950 (pt) REVERT: D 312 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7553 (mp0) REVERT: D 872 ASP cc_start: 0.8771 (t0) cc_final: 0.8452 (t70) REVERT: D 880 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7385 (mt-10) outliers start: 18 outliers final: 12 residues processed: 160 average time/residue: 0.1917 time to fit residues: 45.1348 Evaluate side-chains 160 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 872 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 120 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.099537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083634 restraints weight = 31705.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086112 restraints weight = 18497.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087782 restraints weight = 12807.474| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10176 Z= 0.146 Angle : 0.676 8.388 13704 Z= 0.356 Chirality : 0.041 0.138 1540 Planarity : 0.004 0.041 1792 Dihedral : 5.333 26.950 1376 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1248 helix: 1.52 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.83 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 263 PHE 0.010 0.001 PHE D 251 TYR 0.024 0.002 TYR A 231 ARG 0.006 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 584) hydrogen bonds : angle 4.29188 ( 1752) covalent geometry : bond 0.00333 (10176) covalent geometry : angle 0.67622 (13704) *********************** 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 173 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: A 153 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8508 (mtpp) REVERT: A 285 LEU cc_start: 0.9272 (mm) cc_final: 0.8753 (pt) REVERT: B 877 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6647 (mt-10) REVERT: B 880 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7532 (mm-30) REVERT: C 277 LYS cc_start: 0.8516 (mptt) cc_final: 0.7876 (mptt) REVERT: C 285 LEU cc_start: 0.9374 (mm) cc_final: 0.8897 (pt) REVERT: C 858 MET cc_start: 0.8821 (mmm) cc_final: 0.8616 (mmm) REVERT: C 872 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8569 (t70) REVERT: C 900 GLU cc_start: 0.7962 (tt0) cc_final: 0.7478 (tt0) REVERT: D 285 LEU cc_start: 0.9363 (mm) cc_final: 0.8976 (pt) REVERT: D 312 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7512 (mp0) REVERT: D 872 ASP cc_start: 0.8793 (t0) cc_final: 0.8478 (t70) REVERT: D 880 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7341 (mt-10) REVERT: D 911 LEU cc_start: 0.8545 (tt) cc_final: 0.8342 (mm) outliers start: 19 outliers final: 15 residues processed: 163 average time/residue: 0.1974 time to fit residues: 46.7533 Evaluate side-chains 165 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 332 LEU 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 C residue 872 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.0030 chunk 85 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.3488 ------------------------------------------------------------------------------- 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** ** B 904 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 = 0.3746 r_free = 0.3746 target = 0.100721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084974 restraints weight = 31413.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087464 restraints weight = 18344.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.089109 restraints weight = 12685.801| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 0.050 10176 Z= 0.134 Angle : 0.674 8.378 13704 Z= 0.352 Chirality : 0.040 0.163 1540 Planarity : 0.003 0.039 1792 Dihedral : 5.265 26.853 1376 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.56 % Allowed : 21.52 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1248 helix: 1.56 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.75 (0.26), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 227 PHE 0.010 0.001 PHE D 251 TYR 0.022 0.002 TYR A 231 ARG 0.006 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 584) hydrogen bonds : angle 4.22654 ( 1752) covalent geometry : bond 0.00303 (10176) covalent geometry : angle 0.67417 (13704) *********************** 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 173 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: A 153 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8490 (mtpp) REVERT: A 285 LEU cc_start: 0.9273 (mm) cc_final: 0.8835 (pt) REVERT: B 285 LEU cc_start: 0.9362 (mm) cc_final: 0.8957 (pt) REVERT: B 877 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6482 (mt-10) REVERT: B 880 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7469 (mm-30) REVERT: C 230 GLU cc_start: 0.7703 (mp0) cc_final: 0.6966 (mp0) REVERT: C 277 LYS cc_start: 0.8594 (mptt) cc_final: 0.8342 (mptt) REVERT: C 285 LEU cc_start: 0.9149 (mm) cc_final: 0.8789 (pt) REVERT: C 858 MET cc_start: 0.8821 (mmm) cc_final: 0.8609 (mmm) REVERT: C 900 GLU cc_start: 0.7965 (tt0) cc_final: 0.7487 (tt0) REVERT: D 285 LEU cc_start: 0.9366 (mm) cc_final: 0.8977 (pt) REVERT: D 312 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7436 (mp0) REVERT: D 872 ASP cc_start: 0.8790 (t0) cc_final: 0.8484 (t70) REVERT: D 880 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7294 (mt-10) outliers start: 17 outliers final: 11 residues processed: 165 average time/residue: 0.1962 time to fit residues: 47.2920 Evaluate side-chains 158 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 165 LEU 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 60 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 29 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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** ** B 904 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 = 0.3734 r_free = 0.3734 target = 0.100066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084321 restraints weight = 31857.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086817 restraints weight = 18564.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.088430 restraints weight = 12825.471| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10176 Z= 0.143 Angle : 0.681 9.799 13704 Z= 0.355 Chirality : 0.041 0.255 1540 Planarity : 0.003 0.038 1792 Dihedral : 5.203 26.761 1376 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.10 % Allowed : 22.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1248 helix: 1.59 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.72 (0.27), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 227 PHE 0.010 0.001 PHE D 251 TYR 0.024 0.002 TYR A 231 ARG 0.005 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 584) hydrogen bonds : angle 4.30929 ( 1752) covalent geometry : bond 0.00323 (10176) covalent geometry : angle 0.68089 (13704) ********************** 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 163 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 153 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8503 (mtpp) REVERT: A 285 LEU cc_start: 0.9319 (mm) cc_final: 0.8840 (pt) REVERT: B 285 LEU cc_start: 0.9367 (mm) cc_final: 0.8913 (pt) REVERT: B 319 LYS cc_start: 0.7305 (tttt) cc_final: 0.6736 (tppt) REVERT: B 877 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6546 (mt-10) REVERT: B 880 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7528 (mm-30) REVERT: C 285 LEU cc_start: 0.9209 (mm) cc_final: 0.8738 (pt) REVERT: C 858 MET cc_start: 0.8826 (mmm) cc_final: 0.8622 (mmm) REVERT: C 900 GLU cc_start: 0.8088 (tt0) cc_final: 0.7594 (tt0) REVERT: D 285 LEU cc_start: 0.9377 (mm) cc_final: 0.8982 (pt) REVERT: D 312 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7422 (mp0) REVERT: D 324 CYS cc_start: 0.8911 (p) cc_final: 0.8635 (p) REVERT: D 872 ASP cc_start: 0.8795 (t0) cc_final: 0.8505 (t70) REVERT: D 880 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7322 (mt-10) outliers start: 12 outliers final: 10 residues processed: 159 average time/residue: 0.1877 time to fit residues: 43.7546 Evaluate side-chains 157 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 165 LEU 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 106 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 4 optimal weight: 0.0870 chunk 12 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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** ** B 904 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 = 0.3741 r_free = 0.3741 target = 0.100455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.084885 restraints weight = 31666.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.087376 restraints weight = 18525.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089030 restraints weight = 12781.817| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10176 Z= 0.135 Angle : 0.672 8.822 13704 Z= 0.350 Chirality : 0.040 0.167 1540 Planarity : 0.003 0.037 1792 Dihedral : 5.190 26.661 1376 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.10 % Allowed : 22.62 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1248 helix: 1.63 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.68 (0.27), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 263 PHE 0.010 0.001 PHE D 251 TYR 0.015 0.002 TYR C 250 ARG 0.005 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 584) hydrogen bonds : angle 4.21249 ( 1752) covalent geometry : bond 0.00307 (10176) covalent geometry : angle 0.67219 (13704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.82 seconds wall clock time: 60 minutes 11.56 seconds (3611.56 seconds total)