Starting phenix.real_space_refine on Fri Feb 14 09:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cv9_7637/02_2025/6cv9_7637.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cv9_7637/02_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_7637/02_2025/6cv9_7637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cv9_7637/02_2025/6cv9_7637.map" model { file = "/net/cci-nas-00/data/ceres_data/6cv9_7637/02_2025/6cv9_7637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cv9_7637/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.74, per 1000 atoms: 0.47 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: 2.52 Conformation dependent library (CDL) restraints added in 1.2 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: 0.95 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: 2.58 Time building geometry restraints manager: 2.94 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: 0.700 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.040 Find NCS groups from input model: 0.200 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- 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= 0.406 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 *********************** 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 : 1.160 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: 0.3151 time to fit residues: 187.5125 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 : 1.527 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089881 restraints weight = 31540.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.092504 restraints weight = 18765.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.094239 restraints weight = 13097.794| |-----------------------------------------------------------------------------| 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= 0.232 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 *********************** 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 : 1.186 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: 0.8168 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 277 LYS cc_start: 0.8359 (mmpt) cc_final: 0.7920 (mmpt) REVERT: A 285 LEU cc_start: 0.9308 (mm) cc_final: 0.8931 (pt) REVERT: A 288 SER cc_start: 0.8720 (p) cc_final: 0.8187 (p) REVERT: A 858 MET cc_start: 0.8685 (mmm) cc_final: 0.8410 (tpp) REVERT: A 872 ASP cc_start: 0.8752 (t0) cc_final: 0.8538 (t70) REVERT: A 911 LEU cc_start: 0.8590 (tt) cc_final: 0.8353 (mt) REVERT: B 128 VAL cc_start: 0.7158 (t) cc_final: 0.6895 (p) REVERT: B 876 ASP cc_start: 0.8307 (p0) cc_final: 0.8078 (p0) REVERT: B 877 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6636 (mt-10) REVERT: C 128 VAL cc_start: 0.7257 (t) cc_final: 0.6992 (p) REVERT: C 900 GLU cc_start: 0.7706 (tt0) cc_final: 0.7482 (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: 0.2057 time to fit residues: 74.2929 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 : 1.157 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 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: 0.6580 ------------------------------------------------------------------------------- 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 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 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.103779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087304 restraints weight = 31824.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.089891 restraints weight = 18920.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091604 restraints weight = 13231.969| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10176 Z= 0.224 Angle : 0.711 7.729 13704 Z= 0.374 Chirality : 0.041 0.173 1540 Planarity : 0.004 0.030 1792 Dihedral : 5.793 20.918 1376 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % 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: -0.94 (0.23), residues: 1248 helix: 0.66 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -3.71 (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 B 107 ARG 0.005 0.001 ARG A 100 *********************** 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 : 1.189 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: 0.7941 (t) cc_final: 0.7732 (p) REVERT: A 285 LEU cc_start: 0.9273 (mm) cc_final: 0.8873 (pt) REVERT: A 319 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8414 (tttt) REVERT: A 858 MET cc_start: 0.8628 (mmm) cc_final: 0.8264 (tpp) REVERT: A 911 LEU cc_start: 0.8893 (tt) cc_final: 0.8608 (mm) REVERT: B 252 CYS cc_start: 0.9255 (t) cc_final: 0.8947 (t) REVERT: B 277 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7731 (mmtm) REVERT: C 128 VAL cc_start: 0.7436 (t) cc_final: 0.7196 (p) REVERT: C 858 MET cc_start: 0.8833 (mmm) cc_final: 0.8612 (mmm) REVERT: C 911 LEU cc_start: 0.8243 (tt) cc_final: 0.8031 (mt) REVERT: D 128 VAL cc_start: 0.7795 (t) cc_final: 0.7490 (p) REVERT: D 252 CYS cc_start: 0.9316 (t) cc_final: 0.9033 (t) REVERT: D 911 LEU cc_start: 0.8491 (tt) cc_final: 0.8287 (mm) outliers start: 28 outliers final: 14 residues processed: 201 average time/residue: 0.2136 time to fit residues: 61.1994 Evaluate side-chains 182 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 86 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS A 904 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 227 HIS D 144 HIS D 217 HIS D 227 HIS ** D 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.101475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084935 restraints weight = 31800.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.087447 restraints weight = 18770.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089092 restraints weight = 13136.589| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10176 Z= 0.230 Angle : 0.681 6.775 13704 Z= 0.359 Chirality : 0.040 0.143 1540 Planarity : 0.004 0.033 1792 Dihedral : 5.591 25.804 1376 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.20 % Allowed : 17.86 % Favored : 79.95 % 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: -0.36 (0.24), residues: 1248 helix: 1.19 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -3.72 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 263 PHE 0.022 0.001 PHE C 251 TYR 0.019 0.002 TYR D 231 ARG 0.004 0.001 ARG A 272 *********************** 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 207 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.223 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 285 LEU cc_start: 0.9285 (mm) cc_final: 0.8792 (pt) REVERT: A 858 MET cc_start: 0.8536 (mmm) cc_final: 0.8182 (tpp) REVERT: B 858 MET cc_start: 0.8975 (mmm) cc_final: 0.8750 (mmm) REVERT: B 880 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7560 (mt-10) REVERT: C 128 VAL cc_start: 0.7713 (t) cc_final: 0.7484 (p) REVERT: C 201 GLN cc_start: 0.5595 (pm20) cc_final: 0.5358 (pm20) REVERT: C 252 CYS cc_start: 0.8998 (t) cc_final: 0.8735 (t) REVERT: C 858 MET cc_start: 0.8798 (mmm) cc_final: 0.8587 (mmm) REVERT: C 911 LEU cc_start: 0.8375 (tt) cc_final: 0.8124 (mt) REVERT: D 285 LEU cc_start: 0.9283 (mm) cc_final: 0.8945 (pt) REVERT: D 312 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7560 (mp0) outliers start: 24 outliers final: 16 residues processed: 195 average time/residue: 0.2459 time to fit residues: 67.1657 Evaluate side-chains 170 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 893 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: 0.7980 chunk 26 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 217 HIS 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 = 0.3764 r_free = 0.3764 target = 0.101563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084959 restraints weight = 31581.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.087508 restraints weight = 18496.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089167 restraints weight = 12890.723| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5783 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= 0.203 Angle : 0.661 9.508 13704 Z= 0.351 Chirality : 0.040 0.166 1540 Planarity : 0.004 0.050 1792 Dihedral : 5.531 25.417 1376 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.11 % Allowed : 19.32 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1248 helix: 1.36 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.77 (0.25), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 263 PHE 0.024 0.001 PHE A 251 TYR 0.020 0.002 TYR B 231 ARG 0.003 0.001 ARG C 894 *********************** 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 186 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.232 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 153 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8838 (mtpp) REVERT: A 285 LEU cc_start: 0.9196 (mm) cc_final: 0.8695 (pt) REVERT: A 858 MET cc_start: 0.8538 (mmm) cc_final: 0.8208 (tpp) REVERT: B 858 MET cc_start: 0.8946 (mmm) cc_final: 0.8745 (mmm) REVERT: B 880 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 128 VAL cc_start: 0.7911 (t) cc_final: 0.7674 (p) REVERT: C 285 LEU cc_start: 0.9301 (mm) cc_final: 0.8897 (pt) REVERT: C 858 MET cc_start: 0.8760 (mmm) cc_final: 0.8539 (mmm) REVERT: C 900 GLU cc_start: 0.7642 (tt0) cc_final: 0.7436 (tt0) REVERT: D 128 VAL cc_start: 0.7866 (t) cc_final: 0.7616 (p) REVERT: D 285 LEU cc_start: 0.9326 (mm) cc_final: 0.8941 (pt) REVERT: D 312 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7453 (mp0) REVERT: D 900 GLU cc_start: 0.7038 (tp30) cc_final: 0.6599 (tp30) REVERT: D 911 LEU cc_start: 0.8456 (tt) cc_final: 0.8214 (mm) outliers start: 23 outliers final: 14 residues processed: 176 average time/residue: 0.2023 time to fit residues: 51.3132 Evaluate side-chains 162 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 885 GLU 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: 2.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- 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 ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.100123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.083607 restraints weight = 31514.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.086094 restraints weight = 18546.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.087696 restraints weight = 12985.241| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.004 0.040 10176 Z= 0.228 Angle : 0.667 8.368 13704 Z= 0.353 Chirality : 0.041 0.161 1540 Planarity : 0.004 0.046 1792 Dihedral : 5.381 26.975 1376 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.84 % Allowed : 19.60 % 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: -0.09 (0.25), residues: 1248 helix: 1.37 (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 0.014 0.001 PHE A 251 TYR 0.026 0.002 TYR A 231 ARG 0.003 0.001 ARG C 190 *********************** 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 188 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9103 (mmmt) cc_final: 0.8836 (mtpp) REVERT: A 285 LEU cc_start: 0.9263 (mm) cc_final: 0.8782 (pt) REVERT: A 900 GLU cc_start: 0.8074 (tt0) cc_final: 0.7640 (tt0) REVERT: B 877 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5985 (mm-30) REVERT: B 880 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 285 LEU cc_start: 0.9337 (mm) cc_final: 0.8900 (pt) REVERT: C 858 MET cc_start: 0.8811 (mmm) cc_final: 0.8590 (mmm) REVERT: C 872 ASP cc_start: 0.8737 (m-30) cc_final: 0.8516 (t0) REVERT: C 880 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 900 GLU cc_start: 0.7913 (tt0) cc_final: 0.7445 (tt0) REVERT: D 285 LEU cc_start: 0.9344 (mm) cc_final: 0.8946 (pt) REVERT: D 312 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7476 (mp0) outliers start: 31 outliers final: 11 residues processed: 177 average time/residue: 0.2080 time to fit residues: 52.4779 Evaluate side-chains 152 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 127 CYS 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 131 MET 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: 3.9990 chunk 72 optimal weight: 0.4980 chunk 32 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.100460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084046 restraints weight = 31923.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086528 restraints weight = 18634.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.088156 restraints weight = 12996.959| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10176 Z= 0.205 Angle : 0.667 10.976 13704 Z= 0.350 Chirality : 0.041 0.218 1540 Planarity : 0.003 0.043 1792 Dihedral : 5.367 26.502 1376 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.92 % Allowed : 20.42 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.25), residues: 1248 helix: 1.65 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.76 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 263 PHE 0.010 0.001 PHE B 205 TYR 0.023 0.002 TYR A 231 ARG 0.003 0.000 ARG D 272 *********************** 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: 21 poor density : 157 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8782 (mtpp) REVERT: A 285 LEU cc_start: 0.9274 (mm) cc_final: 0.8831 (pt) REVERT: B 877 GLU cc_start: 0.6166 (mm-30) cc_final: 0.5901 (mm-30) REVERT: B 880 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7517 (mm-30) REVERT: C 285 LEU cc_start: 0.9327 (mm) cc_final: 0.8879 (pt) REVERT: C 858 MET cc_start: 0.8806 (mmm) cc_final: 0.8602 (mmm) REVERT: C 872 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8525 (t0) REVERT: C 880 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7252 (mm-30) REVERT: D 128 VAL cc_start: 0.7741 (t) cc_final: 0.7514 (p) REVERT: D 285 LEU cc_start: 0.9358 (mm) cc_final: 0.8971 (pt) REVERT: D 312 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7511 (mp0) REVERT: D 872 ASP cc_start: 0.8763 (t0) cc_final: 0.8505 (t70) REVERT: D 880 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7331 (mt-10) outliers start: 21 outliers final: 12 residues processed: 166 average time/residue: 0.1945 time to fit residues: 47.3651 Evaluate side-chains 164 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 127 CYS 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 165 LEU Chi-restraints excluded: chain C residue 872 ASP Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 MET 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 119 optimal weight: 0.0770 chunk 110 optimal weight: 0.6980 chunk 120 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- 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 ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.100428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.084408 restraints weight = 31439.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086910 restraints weight = 18253.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.088511 restraints weight = 12634.898| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6543 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= 0.205 Angle : 0.665 10.452 13704 Z= 0.348 Chirality : 0.040 0.164 1540 Planarity : 0.003 0.038 1792 Dihedral : 5.259 26.613 1376 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.47 % Allowed : 20.97 % 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: 0.24 (0.25), residues: 1248 helix: 1.77 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -3.73 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 263 PHE 0.006 0.001 PHE A 266 TYR 0.020 0.002 TYR A 231 ARG 0.002 0.000 ARG A 894 *********************** 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 175 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8776 (mtpp) REVERT: A 285 LEU cc_start: 0.9291 (mm) cc_final: 0.8779 (pt) REVERT: A 858 MET cc_start: 0.8642 (mmm) cc_final: 0.8176 (tpp) REVERT: A 900 GLU cc_start: 0.7954 (tt0) cc_final: 0.7578 (tt0) REVERT: B 285 LEU cc_start: 0.9332 (mm) cc_final: 0.8904 (pt) REVERT: B 877 GLU cc_start: 0.6108 (mm-30) cc_final: 0.5840 (mm-30) REVERT: B 880 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7538 (mm-30) REVERT: C 285 LEU cc_start: 0.9063 (mm) cc_final: 0.8794 (pt) REVERT: C 319 LYS cc_start: 0.8845 (tppt) cc_final: 0.8623 (mmtt) REVERT: C 858 MET cc_start: 0.8846 (mmm) cc_final: 0.8646 (mmm) REVERT: C 880 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7132 (mm-30) REVERT: D 128 VAL cc_start: 0.7917 (t) cc_final: 0.7694 (p) REVERT: D 285 LEU cc_start: 0.9370 (mm) cc_final: 0.8973 (pt) REVERT: D 312 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7459 (mp0) REVERT: D 872 ASP cc_start: 0.8792 (t0) cc_final: 0.8529 (t70) REVERT: D 880 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7318 (mt-10) outliers start: 16 outliers final: 9 residues processed: 168 average time/residue: 0.1909 time to fit residues: 47.4899 Evaluate side-chains 160 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 127 CYS Chi-restraints excluded: chain B residue 312 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 131 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3724 r_free = 0.3724 target = 0.099446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083705 restraints weight = 31263.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086154 restraints weight = 18229.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.087780 restraints weight = 12618.768| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6710 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= 0.225 Angle : 0.680 11.041 13704 Z= 0.352 Chirality : 0.040 0.165 1540 Planarity : 0.003 0.038 1792 Dihedral : 5.187 26.738 1376 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.19 % Allowed : 21.61 % Favored : 77.20 % 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: 1.76 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.68 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 263 PHE 0.008 0.001 PHE A 266 TYR 0.020 0.002 TYR A 231 ARG 0.003 0.000 ARG C 894 *********************** 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 174 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8807 (mtpp) REVERT: A 285 LEU cc_start: 0.9286 (mm) cc_final: 0.8768 (pt) REVERT: A 858 MET cc_start: 0.8615 (mmm) cc_final: 0.8147 (tpp) REVERT: A 900 GLU cc_start: 0.7959 (tt0) cc_final: 0.7588 (tt0) REVERT: B 285 LEU cc_start: 0.9374 (mm) cc_final: 0.8937 (pt) REVERT: B 880 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7510 (mm-30) REVERT: C 285 LEU cc_start: 0.9069 (mm) cc_final: 0.8753 (pt) REVERT: C 858 MET cc_start: 0.8826 (mmm) cc_final: 0.8618 (mmm) REVERT: C 880 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7282 (mm-30) REVERT: D 285 LEU cc_start: 0.9368 (mm) cc_final: 0.8967 (pt) REVERT: D 312 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7235 (mp0) REVERT: D 872 ASP cc_start: 0.8792 (t0) cc_final: 0.8555 (t70) REVERT: D 880 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7300 (mt-10) outliers start: 13 outliers final: 11 residues processed: 169 average time/residue: 0.2026 time to fit residues: 49.9618 Evaluate side-chains 161 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 127 CYS Chi-restraints excluded: chain B residue 312 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 131 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 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** ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.098398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082789 restraints weight = 31844.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085235 restraints weight = 18569.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.086863 restraints weight = 12814.079| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.6873 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= 0.236 Angle : 0.700 10.069 13704 Z= 0.365 Chirality : 0.041 0.158 1540 Planarity : 0.004 0.041 1792 Dihedral : 5.171 26.343 1376 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.01 % Allowed : 21.70 % Favored : 77.29 % 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: 0.25 (0.25), residues: 1248 helix: 1.73 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.65 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 263 PHE 0.008 0.001 PHE A 266 TYR 0.030 0.002 TYR B 231 ARG 0.002 0.000 ARG A 894 ********************** 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 169 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8809 (mtpp) REVERT: A 285 LEU cc_start: 0.9304 (mm) cc_final: 0.8788 (pt) REVERT: A 858 MET cc_start: 0.8652 (mmm) cc_final: 0.8176 (tpp) REVERT: A 900 GLU cc_start: 0.7981 (tt0) cc_final: 0.7608 (tt0) REVERT: B 285 LEU cc_start: 0.9371 (mm) cc_final: 0.8971 (pt) REVERT: B 298 GLU cc_start: 0.8038 (tt0) cc_final: 0.7488 (tt0) REVERT: B 858 MET cc_start: 0.8676 (mmm) cc_final: 0.8352 (mmm) REVERT: B 877 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6589 (mm-30) REVERT: B 880 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7416 (mm-30) REVERT: C 285 LEU cc_start: 0.9137 (mm) cc_final: 0.8668 (pt) REVERT: C 858 MET cc_start: 0.8836 (mmm) cc_final: 0.8597 (mmm) REVERT: C 880 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7161 (mm-30) REVERT: D 285 LEU cc_start: 0.9401 (mm) cc_final: 0.9002 (pt) REVERT: D 312 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7248 (mp0) REVERT: D 872 ASP cc_start: 0.8811 (t0) cc_final: 0.8575 (t70) REVERT: D 880 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7325 (mt-10) outliers start: 11 outliers final: 8 residues processed: 164 average time/residue: 0.1788 time to fit residues: 43.7210 Evaluate side-chains 157 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 131 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 222 ILE 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: 0.5980 chunk 12 optimal weight: 0.0050 chunk 34 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 112 optimal weight: 0.0030 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.099837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084134 restraints weight = 31758.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086576 restraints weight = 18691.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.088236 restraints weight = 13025.109| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6983 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= 0.201 Angle : 0.701 10.168 13704 Z= 0.362 Chirality : 0.040 0.161 1540 Planarity : 0.003 0.037 1792 Dihedral : 5.147 26.426 1376 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.82 % Allowed : 21.89 % Favored : 77.29 % 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: 0.29 (0.25), residues: 1248 helix: 1.76 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.62 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 227 PHE 0.007 0.001 PHE A 266 TYR 0.030 0.002 TYR C 231 ARG 0.002 0.000 ARG C 894 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.98 seconds wall clock time: 52 minutes 22.63 seconds (3142.63 seconds total)