Starting phenix.real_space_refine on Wed Feb 12 03:05:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5h_20646/02_2025/6u5h_20646.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5h_20646/02_2025/6u5h_20646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5h_20646/02_2025/6u5h_20646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5h_20646/02_2025/6u5h_20646.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5h_20646/02_2025/6u5h_20646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5h_20646/02_2025/6u5h_20646.cif" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.004 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 42 5.16 5 C 4530 2.51 5 N 1362 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2442 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 304} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: C, B Time building chain proxies: 5.07, per 1000 atoms: 0.69 Number of scatterers: 7326 At special positions: 0 Unit cell: (90.567, 94.731, 78.075, 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 42 16.00 O 1392 8.00 N 1362 7.00 C 4530 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: 1.68 Conformation dependent library (CDL) restraints added in 984.5 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 10.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN C 176 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER C 177 " --> pdb=" O PRO C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 177' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 256' Processing helix chain 'C' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.754A pdb=" N ASP B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 177 " --> pdb=" O PRO B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 173 through 177' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.609A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.993A pdb=" N ARG B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.753A pdb=" N ASP A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.661A pdb=" N GLN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.610A pdb=" N GLU A 255 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.994A pdb=" N ARG A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 8 removed outlier: 3.668A pdb=" N GLY C 63 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 73 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 62 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ARG C 71 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG C 41 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU C 25 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR C 39 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191 removed outlier: 5.676A pdb=" N ILE C 303 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN C 322 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY B 63 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 73 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 62 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG B 71 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG B 41 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 25 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N THR B 39 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE B 303 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 322 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 8 removed outlier: 3.667A pdb=" N GLY A 63 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 73 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 62 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ARG A 71 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 22 through 26 removed outlier: 6.357A pdb=" N ARG A 41 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 25 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191 removed outlier: 5.675A pdb=" N ILE A 303 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN A 322 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 202 through 203 81 hydrogen bonds defined for protein. 225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2539 1.34 - 1.46: 1375 1.46 - 1.58: 3460 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 7443 Sorted by residual: bond pdb=" C LEU A 218 " pdb=" N PRO A 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.76e+00 bond pdb=" CB PRO A 86 " pdb=" CG PRO A 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" CB PRO C 86 " pdb=" CG PRO C 86 " ideal model delta sigma weight residual 1.492 1.426 0.066 5.00e-02 4.00e+02 1.75e+00 bond pdb=" C LEU B 218 " pdb=" N PRO B 219 " ideal model delta sigma weight residual 1.341 1.362 -0.021 1.60e-02 3.91e+03 1.66e+00 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 9573 2.10 - 4.20: 387 4.20 - 6.30: 48 6.30 - 8.39: 26 8.39 - 10.49: 19 Bond angle restraints: 10053 Sorted by residual: angle pdb=" N VAL B 14 " pdb=" CA VAL B 14 " pdb=" C VAL B 14 " ideal model delta sigma weight residual 108.95 101.03 7.92 1.65e+00 3.67e-01 2.31e+01 angle pdb=" N VAL A 14 " pdb=" CA VAL A 14 " pdb=" C VAL A 14 " ideal model delta sigma weight residual 108.95 101.07 7.88 1.65e+00 3.67e-01 2.28e+01 angle pdb=" N VAL C 14 " pdb=" CA VAL C 14 " pdb=" C VAL C 14 " ideal model delta sigma weight residual 108.95 101.09 7.86 1.65e+00 3.67e-01 2.27e+01 angle pdb=" CA PRO A 85 " pdb=" C PRO A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 117.93 123.03 -5.10 1.20e+00 6.94e-01 1.81e+01 angle pdb=" CA PRO B 85 " pdb=" C PRO B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 117.93 123.00 -5.07 1.20e+00 6.94e-01 1.78e+01 ... (remaining 10048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 4254 14.28 - 28.55: 249 28.55 - 42.83: 9 42.83 - 57.10: 0 57.10 - 71.38: 6 Dihedral angle restraints: 4518 sinusoidal: 1830 harmonic: 2688 Sorted by residual: dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta harmonic sigma weight residual 180.00 154.32 25.68 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA PHE A 199 " pdb=" C PHE A 199 " pdb=" N ASP A 200 " pdb=" CA ASP A 200 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PHE C 199 " pdb=" C PHE C 199 " pdb=" N ASP C 200 " pdb=" CA ASP C 200 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 4515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 824 0.058 - 0.117: 229 0.117 - 0.175: 61 0.175 - 0.233: 8 0.233 - 0.292: 3 Chirality restraints: 1125 Sorted by residual: chirality pdb=" CB ILE C 105 " pdb=" CA ILE C 105 " pdb=" CG1 ILE C 105 " pdb=" CG2 ILE C 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE B 105 " pdb=" CA ILE B 105 " pdb=" CG1 ILE B 105 " pdb=" CG2 ILE B 105 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1122 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 187 " 0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 187 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 188 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 188 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " 0.035 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1109 2.77 - 3.30: 6094 3.30 - 3.83: 11304 3.83 - 4.37: 13014 4.37 - 4.90: 22207 Nonbonded interactions: 53728 Sorted by model distance: nonbonded pdb=" OG1 THR B 79 " pdb=" OG1 THR B 92 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR C 79 " pdb=" OG1 THR C 92 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR A 79 " pdb=" OG1 THR A 92 " model vdw 2.234 3.040 nonbonded pdb=" O THR B 104 " pdb=" OG1 THR B 153 " model vdw 2.246 3.040 nonbonded pdb=" O THR C 104 " pdb=" OG1 THR C 153 " model vdw 2.247 3.040 ... (remaining 53723 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 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 : 0.005 0.066 7443 Z= 0.355 Angle : 1.067 10.493 10053 Z= 0.571 Chirality : 0.059 0.292 1125 Planarity : 0.006 0.063 1326 Dihedral : 8.739 71.380 2796 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % Favored : 99.23 % 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: -5.23 (0.22), residues: 942 helix: -5.41 (0.09), residues: 90 sheet: -3.34 (0.32), residues: 213 loop : -3.43 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 315 HIS 0.006 0.002 HIS C 150 PHE 0.011 0.002 PHE A 151 TYR 0.023 0.002 TYR C 310 ARG 0.006 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 223 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8442 (p) cc_final: 0.8184 (p) REVERT: C 198 SER cc_start: 0.8614 (p) cc_final: 0.8385 (m) REVERT: C 215 ARG cc_start: 0.6463 (mtt180) cc_final: 0.5761 (mmm160) REVERT: B 44 ASP cc_start: 0.8156 (m-30) cc_final: 0.7889 (m-30) REVERT: B 48 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7931 (mm-40) REVERT: B 64 TYR cc_start: 0.8561 (m-10) cc_final: 0.8121 (m-10) REVERT: B 215 ARG cc_start: 0.6355 (mtt180) cc_final: 0.5448 (mmm160) REVERT: B 289 LEU cc_start: 0.7809 (mt) cc_final: 0.7508 (mt) REVERT: A 205 ASP cc_start: 0.7634 (m-30) cc_final: 0.7286 (m-30) REVERT: A 215 ARG cc_start: 0.6525 (mtt180) cc_final: 0.5844 (mmp-170) REVERT: A 281 ASP cc_start: 0.7677 (m-30) cc_final: 0.7103 (m-30) outliers start: 3 outliers final: 0 residues processed: 226 average time/residue: 0.2926 time to fit residues: 80.4662 Evaluate side-chains 135 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 242 HIS B 81 GLN B 242 HIS A 242 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.226013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.181717 restraints weight = 7866.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.182452 restraints weight = 7053.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.182883 restraints weight = 6528.278| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7443 Z= 0.282 Angle : 0.769 7.440 10053 Z= 0.392 Chirality : 0.047 0.134 1125 Planarity : 0.006 0.048 1326 Dihedral : 7.189 25.760 1059 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.22 % Allowed : 7.98 % Favored : 88.80 % 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: -5.11 (0.22), residues: 942 helix: -5.13 (0.18), residues: 96 sheet: -3.57 (0.26), residues: 267 loop : -3.08 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 315 HIS 0.003 0.001 HIS A 246 PHE 0.015 0.002 PHE C 265 TYR 0.020 0.002 TYR A 159 ARG 0.004 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7192 (mtt180) cc_final: 0.6940 (mmt90) REVERT: C 205 ASP cc_start: 0.7892 (m-30) cc_final: 0.7566 (m-30) REVERT: C 215 ARG cc_start: 0.6477 (mtt180) cc_final: 0.5877 (mmm160) REVERT: C 322 ASN cc_start: 0.7186 (m110) cc_final: 0.6733 (m110) REVERT: B 215 ARG cc_start: 0.6167 (mtt180) cc_final: 0.5491 (mmm160) REVERT: B 302 LEU cc_start: 0.8508 (mt) cc_final: 0.8176 (mt) REVERT: B 322 ASN cc_start: 0.6921 (m110) cc_final: 0.6486 (m110) REVERT: A 120 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6271 (mmt90) REVERT: A 205 ASP cc_start: 0.7763 (m-30) cc_final: 0.7261 (m-30) REVERT: A 215 ARG cc_start: 0.6518 (mtt180) cc_final: 0.5953 (mmm160) REVERT: A 259 LYS cc_start: 0.5925 (mttt) cc_final: 0.5579 (mmtp) outliers start: 25 outliers final: 19 residues processed: 171 average time/residue: 0.2431 time to fit residues: 52.7591 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 55 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 0.0570 chunk 49 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 overall best weight: 1.1040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.229244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.185598 restraints weight = 7965.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.186514 restraints weight = 6775.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.187333 restraints weight = 6148.378| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7443 Z= 0.169 Angle : 0.693 8.764 10053 Z= 0.346 Chirality : 0.045 0.137 1125 Planarity : 0.004 0.041 1326 Dihedral : 6.476 23.385 1059 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 2.45 % Allowed : 11.97 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.81 (0.22), residues: 942 helix: -4.84 (0.28), residues: 96 sheet: -3.25 (0.27), residues: 279 loop : -2.93 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 150 PHE 0.015 0.001 PHE C 265 TYR 0.010 0.001 TYR B 159 ARG 0.005 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6890 (mmt90) REVERT: C 169 MET cc_start: 0.3230 (mmt) cc_final: 0.3016 (mmt) REVERT: C 215 ARG cc_start: 0.6475 (mtt180) cc_final: 0.5842 (mmm160) REVERT: C 322 ASN cc_start: 0.7421 (m110) cc_final: 0.7186 (m110) REVERT: B 215 ARG cc_start: 0.6271 (mtt180) cc_final: 0.5559 (mmm160) REVERT: B 275 GLU cc_start: 0.8011 (tt0) cc_final: 0.7623 (mt-10) REVERT: B 310 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6688 (m-10) REVERT: A 120 ARG cc_start: 0.6832 (mtt90) cc_final: 0.6454 (mmt90) REVERT: A 205 ASP cc_start: 0.7692 (m-30) cc_final: 0.6979 (m-30) REVERT: A 215 ARG cc_start: 0.6722 (mtt180) cc_final: 0.6098 (mmm160) REVERT: A 259 LYS cc_start: 0.5866 (mttt) cc_final: 0.5561 (mmtp) outliers start: 19 outliers final: 12 residues processed: 162 average time/residue: 0.2542 time to fit residues: 52.0708 Evaluate side-chains 150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 71 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 67 optimal weight: 0.0370 chunk 44 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 179 GLN C 246 HIS B 246 HIS A 81 GLN A 179 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.218594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.184675 restraints weight = 8168.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182321 restraints weight = 11778.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.182150 restraints weight = 11528.035| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7443 Z= 0.375 Angle : 0.802 9.409 10053 Z= 0.405 Chirality : 0.048 0.137 1125 Planarity : 0.007 0.053 1326 Dihedral : 6.877 26.171 1059 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer: Outliers : 3.47 % Allowed : 13.00 % Favored : 83.53 % 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: -5.00 (0.22), residues: 942 helix: -5.05 (0.15), residues: 114 sheet: -3.38 (0.28), residues: 276 loop : -2.94 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 315 HIS 0.004 0.001 HIS B 246 PHE 0.018 0.002 PHE A 265 TYR 0.015 0.002 TYR B 159 ARG 0.007 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 289 LEU cc_start: 0.8263 (mt) cc_final: 0.7929 (mt) REVERT: A 215 ARG cc_start: 0.6191 (mtt180) cc_final: 0.5929 (mmm160) REVERT: A 259 LYS cc_start: 0.6139 (mttt) cc_final: 0.5843 (mmtt) outliers start: 27 outliers final: 23 residues processed: 165 average time/residue: 0.2355 time to fit residues: 49.3762 Evaluate side-chains 157 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** 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 = 0.4339 r_free = 0.4339 target = 0.219531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.182073 restraints weight = 8119.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.180137 restraints weight = 12400.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.181215 restraints weight = 10923.821| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7443 Z= 0.289 Angle : 0.729 7.621 10053 Z= 0.367 Chirality : 0.046 0.138 1125 Planarity : 0.005 0.044 1326 Dihedral : 6.552 24.891 1059 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 4.25 % Allowed : 15.44 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.98 (0.23), residues: 942 helix: -4.98 (0.15), residues: 120 sheet: -3.33 (0.27), residues: 297 loop : -2.87 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 82 HIS 0.004 0.001 HIS C 246 PHE 0.019 0.002 PHE A 265 TYR 0.010 0.001 TYR B 216 ARG 0.008 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 ARG cc_start: 0.6349 (mtt180) cc_final: 0.5958 (mmm160) REVERT: C 300 GLU cc_start: 0.8301 (tp30) cc_final: 0.8054 (tp30) REVERT: C 322 ASN cc_start: 0.7140 (m110) cc_final: 0.6869 (m110) REVERT: B 169 MET cc_start: 0.3707 (mmt) cc_final: 0.3209 (mmt) REVERT: B 294 LYS cc_start: 0.4964 (OUTLIER) cc_final: 0.4423 (mtpt) REVERT: B 310 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6538 (m-10) REVERT: B 316 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7658 (p) REVERT: A 215 ARG cc_start: 0.6271 (mtt180) cc_final: 0.5874 (mmm160) REVERT: A 259 LYS cc_start: 0.6012 (mttt) cc_final: 0.5684 (mmtp) outliers start: 33 outliers final: 21 residues processed: 152 average time/residue: 0.2590 time to fit residues: 49.5189 Evaluate side-chains 146 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 87 optimal weight: 20.0000 chunk 25 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** 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 = 0.4395 r_free = 0.4395 target = 0.225121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.189043 restraints weight = 8029.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.187281 restraints weight = 12547.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.187679 restraints weight = 10809.379| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7443 Z= 0.164 Angle : 0.663 8.918 10053 Z= 0.329 Chirality : 0.044 0.172 1125 Planarity : 0.004 0.042 1326 Dihedral : 5.865 20.957 1059 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.70 % Allowed : 17.37 % Favored : 79.92 % 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: -4.62 (0.24), residues: 942 helix: -4.85 (0.19), residues: 102 sheet: -3.05 (0.27), residues: 300 loop : -2.73 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 150 PHE 0.012 0.001 PHE A 265 TYR 0.009 0.001 TYR B 216 ARG 0.006 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 ARG cc_start: 0.6473 (mtt180) cc_final: 0.6019 (mmm160) REVERT: C 300 GLU cc_start: 0.8024 (tp30) cc_final: 0.7754 (tp30) REVERT: B 120 ARG cc_start: 0.7174 (mmt180) cc_final: 0.6827 (mpt180) REVERT: B 289 LEU cc_start: 0.8296 (mt) cc_final: 0.7934 (mt) REVERT: B 310 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6332 (m-10) REVERT: A 210 ARG cc_start: 0.6035 (mmt180) cc_final: 0.4815 (mtt-85) REVERT: A 215 ARG cc_start: 0.6349 (mtt180) cc_final: 0.5979 (mmm160) REVERT: A 259 LYS cc_start: 0.5875 (mttt) cc_final: 0.5580 (mmtp) outliers start: 21 outliers final: 14 residues processed: 152 average time/residue: 0.2736 time to fit residues: 51.6074 Evaluate side-chains 154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 72 optimal weight: 0.0030 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 40.0000 chunk 49 optimal weight: 0.0470 chunk 85 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 158 GLN B 81 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.224154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.185634 restraints weight = 7972.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.180479 restraints weight = 8777.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.181018 restraints weight = 9705.402| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7443 Z= 0.171 Angle : 0.641 7.725 10053 Z= 0.318 Chirality : 0.044 0.157 1125 Planarity : 0.004 0.040 1326 Dihedral : 5.681 20.183 1059 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.45 % Allowed : 18.02 % Favored : 79.54 % 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: -4.58 (0.24), residues: 942 helix: -4.89 (0.18), residues: 111 sheet: -2.95 (0.27), residues: 300 loop : -2.68 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 150 PHE 0.008 0.001 PHE A 265 TYR 0.005 0.001 TYR B 310 ARG 0.008 0.000 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 MET cc_start: 0.6026 (mtt) cc_final: 0.5716 (ptp) REVERT: C 215 ARG cc_start: 0.6559 (mtt180) cc_final: 0.6028 (mmm160) REVERT: C 300 GLU cc_start: 0.8001 (tp30) cc_final: 0.7738 (tp30) REVERT: B 289 LEU cc_start: 0.8304 (mt) cc_final: 0.7924 (mt) REVERT: B 310 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: A 209 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6406 (mtt) REVERT: A 215 ARG cc_start: 0.6532 (mtt180) cc_final: 0.5912 (mmm160) REVERT: A 259 LYS cc_start: 0.6031 (mttt) cc_final: 0.5626 (mmtp) outliers start: 19 outliers final: 12 residues processed: 152 average time/residue: 0.2795 time to fit residues: 52.2406 Evaluate side-chains 142 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 73 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 40.0000 chunk 57 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN A 81 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.219154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.183160 restraints weight = 8025.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.182188 restraints weight = 12663.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.182519 restraints weight = 10854.393| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7443 Z= 0.305 Angle : 0.710 7.887 10053 Z= 0.357 Chirality : 0.046 0.156 1125 Planarity : 0.005 0.048 1326 Dihedral : 6.056 22.719 1059 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 3.86 % Allowed : 18.02 % Favored : 78.12 % 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: -4.72 (0.24), residues: 942 helix: -4.96 (0.17), residues: 111 sheet: -3.13 (0.27), residues: 303 loop : -2.71 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 315 HIS 0.003 0.001 HIS A 246 PHE 0.012 0.002 PHE A 199 TYR 0.009 0.001 TYR C 310 ARG 0.008 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.4225 (mt-10) REVERT: C 300 GLU cc_start: 0.8127 (tp30) cc_final: 0.7924 (tp30) REVERT: B 120 ARG cc_start: 0.7438 (mpt180) cc_final: 0.6858 (mpt180) REVERT: B 310 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: A 120 ARG cc_start: 0.6509 (mtt180) cc_final: 0.6211 (mtt180) REVERT: A 209 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6233 (mtt) REVERT: A 215 ARG cc_start: 0.6309 (mtt180) cc_final: 0.5932 (mmm160) REVERT: A 259 LYS cc_start: 0.5933 (mttt) cc_final: 0.5566 (mmtp) outliers start: 30 outliers final: 22 residues processed: 146 average time/residue: 0.2915 time to fit residues: 52.4168 Evaluate side-chains 148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** 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 = 0.4307 r_free = 0.4307 target = 0.214286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179652 restraints weight = 8178.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.177572 restraints weight = 13044.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.175780 restraints weight = 12717.310| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7443 Z= 0.333 Angle : 0.745 8.468 10053 Z= 0.376 Chirality : 0.047 0.159 1125 Planarity : 0.006 0.057 1326 Dihedral : 6.356 26.785 1059 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 4.12 % Allowed : 18.02 % Favored : 77.86 % 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: -4.79 (0.24), residues: 942 helix: -4.91 (0.18), residues: 105 sheet: -3.14 (0.28), residues: 294 loop : -2.87 (0.23), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 315 HIS 0.004 0.001 HIS A 246 PHE 0.015 0.002 PHE A 199 TYR 0.013 0.002 TYR B 159 ARG 0.010 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 GLU cc_start: 0.4793 (OUTLIER) cc_final: 0.4553 (mt-10) REVERT: C 210 ARG cc_start: 0.6449 (mmt-90) cc_final: 0.5652 (tpp-160) REVERT: B 209 MET cc_start: 0.6107 (mtt) cc_final: 0.5878 (mtt) REVERT: B 310 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6560 (m-10) REVERT: B 322 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6775 (m110) REVERT: A 209 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5992 (mtt) REVERT: A 215 ARG cc_start: 0.6157 (mtt180) cc_final: 0.5827 (mmm160) REVERT: A 230 LYS cc_start: 0.4759 (tptp) cc_final: 0.4460 (mttt) REVERT: A 259 LYS cc_start: 0.5954 (mttt) cc_final: 0.5683 (mmtp) outliers start: 32 outliers final: 25 residues processed: 146 average time/residue: 0.3026 time to fit residues: 54.3770 Evaluate side-chains 153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 80 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 74 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** 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 = 0.4337 r_free = 0.4337 target = 0.218374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.184773 restraints weight = 8162.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.181087 restraints weight = 12709.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.180813 restraints weight = 11907.311| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7443 Z= 0.220 Angle : 0.680 7.453 10053 Z= 0.341 Chirality : 0.046 0.160 1125 Planarity : 0.005 0.040 1326 Dihedral : 5.970 23.923 1059 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 3.47 % Allowed : 18.40 % Favored : 78.12 % 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: -4.65 (0.24), residues: 942 helix: -4.85 (0.19), residues: 105 sheet: -2.94 (0.28), residues: 294 loop : -2.84 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 315 HIS 0.002 0.001 HIS A 246 PHE 0.009 0.001 PHE A 199 TYR 0.006 0.001 TYR B 310 ARG 0.014 0.001 ARG B 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 GLU cc_start: 0.4724 (OUTLIER) cc_final: 0.4514 (mt-10) REVERT: B 209 MET cc_start: 0.6200 (mtt) cc_final: 0.5948 (mtt) REVERT: B 310 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6411 (m-10) REVERT: B 322 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6665 (m110) REVERT: A 230 LYS cc_start: 0.4729 (tptp) cc_final: 0.4484 (mttt) REVERT: A 259 LYS cc_start: 0.5931 (mttt) cc_final: 0.5683 (mmtp) outliers start: 27 outliers final: 22 residues processed: 140 average time/residue: 0.3102 time to fit residues: 52.6782 Evaluate side-chains 146 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 199 PHE Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 79 optimal weight: 0.0470 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 HIS ** 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 = 0.4342 r_free = 0.4342 target = 0.218988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.184774 restraints weight = 8012.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.177782 restraints weight = 11275.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.174070 restraints weight = 9458.349| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7443 Z= 0.229 Angle : 0.683 9.431 10053 Z= 0.341 Chirality : 0.045 0.156 1125 Planarity : 0.005 0.065 1326 Dihedral : 5.921 22.929 1059 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 3.60 % Allowed : 18.40 % Favored : 77.99 % 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: -4.78 (0.24), residues: 942 helix: -4.57 (0.24), residues: 123 sheet: -2.94 (0.28), residues: 306 loop : -2.97 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 315 HIS 0.002 0.001 HIS A 246 PHE 0.010 0.001 PHE A 199 TYR 0.010 0.001 TYR C 159 ARG 0.013 0.001 ARG B 157 =============================================================================== Job complete usr+sys time: 2352.53 seconds wall clock time: 42 minutes 51.73 seconds (2571.73 seconds total)