Starting phenix.real_space_refine on Tue Feb 13 18:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2024/6u5h_20646.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2024/6u5h_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2024/6u5h_20646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2024/6u5h_20646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2024/6u5h_20646.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u5h_20646/02_2024/6u5h_20646.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" 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 Chain: "B" 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 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 Time building chain proxies: 4.27, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 2.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.77 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: 1.80 Time building geometry restraints manager: 2.84 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: 99.43 - 106.64: 234 106.64 - 113.85: 4131 113.85 - 121.07: 3250 121.07 - 128.28: 2381 128.28 - 135.49: 57 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 2.440 nonbonded pdb=" OG1 THR C 79 " pdb=" OG1 THR C 92 " model vdw 2.234 2.440 nonbonded pdb=" OG1 THR A 79 " pdb=" OG1 THR A 92 " model vdw 2.234 2.440 nonbonded pdb=" O THR B 104 " pdb=" OG1 THR B 153 " model vdw 2.246 2.440 nonbonded pdb=" O THR C 104 " pdb=" OG1 THR C 153 " model vdw 2.247 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 7.250 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.780 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 0.739 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: 0.2819 time to fit residues: 77.5045 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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: 30.0000 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 50.0000 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 chunk 54 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN C 242 HIS B 81 GLN B 126 ASN B 242 HIS A 126 ASN A 242 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7443 Z= 0.332 Angle : 0.767 7.013 10053 Z= 0.392 Chirality : 0.048 0.131 1125 Planarity : 0.006 0.047 1326 Dihedral : 7.142 26.727 1059 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 3.60 % Allowed : 8.37 % Favored : 88.03 % 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: -5.18 (0.22), residues: 942 helix: -5.26 (0.15), residues: 96 sheet: -3.61 (0.27), residues: 270 loop : -3.12 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP C 315 HIS 0.004 0.001 HIS A 246 PHE 0.016 0.002 PHE C 265 TYR 0.020 0.003 TYR A 159 ARG 0.003 0.001 ARG C 6 *********************** 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 183 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7272 (mtt180) cc_final: 0.7006 (mmt90) REVERT: C 205 ASP cc_start: 0.8034 (m-30) cc_final: 0.7654 (m-30) REVERT: C 210 ARG cc_start: 0.6588 (mmt-90) cc_final: 0.6370 (mmt-90) REVERT: C 215 ARG cc_start: 0.6350 (mtt180) cc_final: 0.5737 (mmm160) REVERT: B 120 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6822 (mmt180) REVERT: B 215 ARG cc_start: 0.6193 (mtt180) cc_final: 0.5217 (mmm160) REVERT: B 302 LEU cc_start: 0.8560 (mt) cc_final: 0.8208 (mt) REVERT: B 322 ASN cc_start: 0.7058 (m110) cc_final: 0.6734 (m110) REVERT: A 120 ARG cc_start: 0.7049 (mmt90) cc_final: 0.6603 (mmt90) REVERT: A 205 ASP cc_start: 0.7836 (m-30) cc_final: 0.7348 (m-30) REVERT: A 215 ARG cc_start: 0.6547 (mtt180) cc_final: 0.5793 (mmm160) REVERT: A 259 LYS cc_start: 0.5900 (mttt) cc_final: 0.5480 (mmtp) outliers start: 28 outliers final: 21 residues processed: 173 average time/residue: 0.2471 time to fit residues: 53.7974 Evaluate side-chains 158 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR 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 46 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 75 optimal weight: 50.0000 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN B 126 ASN A 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7443 Z= 0.246 Angle : 0.722 9.634 10053 Z= 0.361 Chirality : 0.046 0.139 1125 Planarity : 0.005 0.044 1326 Dihedral : 6.673 25.131 1059 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 3.99 % Allowed : 12.23 % Favored : 83.78 % 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: -5.19 (0.13), residues: 114 sheet: -3.42 (0.27), residues: 282 loop : -3.01 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 82 HIS 0.004 0.001 HIS A 246 PHE 0.022 0.002 PHE A 265 TYR 0.012 0.002 TYR B 159 ARG 0.006 0.000 ARG C 157 *********************** 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 165 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7259 (mtt180) cc_final: 0.6973 (mmt90) REVERT: C 215 ARG cc_start: 0.6447 (mtt180) cc_final: 0.5678 (mmm160) REVERT: B 1 MET cc_start: 0.7163 (mmp) cc_final: 0.6843 (mmm) REVERT: B 120 ARG cc_start: 0.7009 (mtt180) cc_final: 0.6721 (mmt-90) REVERT: B 157 ARG cc_start: 0.4211 (mmm160) cc_final: 0.3769 (mmm160) REVERT: B 215 ARG cc_start: 0.6254 (mtt180) cc_final: 0.5297 (mmm160) REVERT: B 302 LEU cc_start: 0.8522 (mt) cc_final: 0.8195 (mt) REVERT: B 310 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6640 (m-10) REVERT: B 315 TRP cc_start: 0.8035 (m-10) cc_final: 0.7703 (m-10) REVERT: A 120 ARG cc_start: 0.6929 (mtt90) cc_final: 0.6634 (mmt90) REVERT: A 205 ASP cc_start: 0.7819 (m-30) cc_final: 0.7178 (m-30) REVERT: A 215 ARG cc_start: 0.6608 (mtt180) cc_final: 0.5763 (mmm160) REVERT: A 259 LYS cc_start: 0.5927 (mttt) cc_final: 0.5496 (mmtp) outliers start: 31 outliers final: 23 residues processed: 149 average time/residue: 0.2545 time to fit residues: 47.8786 Evaluate side-chains 147 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 272 VAL Chi-restraints excluded: chain C residue 281 ASP 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 198 SER 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 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 209 MET 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 83 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 43 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 24 optimal weight: 20.0000 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3707 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= 0.215 Angle : 0.675 10.289 10053 Z= 0.336 Chirality : 0.045 0.135 1125 Planarity : 0.005 0.044 1326 Dihedral : 6.207 23.492 1059 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 4.38 % Allowed : 14.41 % Favored : 81.21 % 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: -5.04 (0.22), residues: 942 helix: -5.06 (0.13), residues: 132 sheet: -3.24 (0.28), residues: 282 loop : -2.95 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 82 HIS 0.002 0.001 HIS A 246 PHE 0.022 0.001 PHE B 265 TYR 0.009 0.001 TYR A 310 ARG 0.007 0.000 ARG C 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 170 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.821 Fit side-chains REVERT: C 120 ARG cc_start: 0.7321 (mtt180) cc_final: 0.7002 (mmt90) REVERT: C 209 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6509 (mtt) REVERT: C 210 ARG cc_start: 0.6422 (mmt-90) cc_final: 0.6166 (mmt-90) REVERT: C 215 ARG cc_start: 0.6462 (mtt180) cc_final: 0.5759 (mmm160) REVERT: B 120 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6736 (mmt-90) REVERT: B 275 GLU cc_start: 0.7949 (tt0) cc_final: 0.7538 (tt0) REVERT: B 310 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: A 120 ARG cc_start: 0.7001 (mtt90) cc_final: 0.6753 (mmt90) REVERT: A 205 ASP cc_start: 0.7786 (m-30) cc_final: 0.7065 (m-30) REVERT: A 215 ARG cc_start: 0.6559 (mtt180) cc_final: 0.5720 (mmm160) REVERT: A 259 LYS cc_start: 0.5952 (mttt) cc_final: 0.5508 (mmtp) outliers start: 34 outliers final: 28 residues processed: 157 average time/residue: 0.2424 time to fit residues: 48.2171 Evaluate side-chains 158 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 317 THR 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 198 SER Chi-restraints excluded: chain B residue 204 ASP 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 317 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 ASP 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 155 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.0670 chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 158 GLN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS B 308 HIS A 81 GLN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.4261 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= 0.323 Angle : 0.741 9.747 10053 Z= 0.371 Chirality : 0.046 0.137 1125 Planarity : 0.006 0.047 1326 Dihedral : 6.429 24.929 1059 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 5.53 % Allowed : 15.44 % Favored : 79.02 % 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: -4.99 (0.23), residues: 942 helix: -4.96 (0.16), residues: 132 sheet: -3.21 (0.28), residues: 297 loop : -2.90 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 315 HIS 0.004 0.001 HIS A 246 PHE 0.016 0.002 PHE A 265 TYR 0.009 0.001 TYR C 310 ARG 0.009 0.001 ARG C 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 168 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: C 210 ARG cc_start: 0.6438 (mmt-90) cc_final: 0.6200 (mmt-90) REVERT: B 120 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6645 (mmt-90) REVERT: B 157 ARG cc_start: 0.4046 (mmm160) cc_final: 0.3761 (mmm160) REVERT: B 294 LYS cc_start: 0.4956 (OUTLIER) cc_final: 0.4657 (mtpt) REVERT: B 310 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.6695 (m-10) REVERT: A 215 ARG cc_start: 0.6625 (mtt180) cc_final: 0.5600 (mmm160) REVERT: A 230 LYS cc_start: 0.3274 (mttt) cc_final: 0.2753 (tppp) REVERT: A 259 LYS cc_start: 0.5997 (mttt) cc_final: 0.5531 (mmtp) outliers start: 43 outliers final: 31 residues processed: 153 average time/residue: 0.2567 time to fit residues: 49.2113 Evaluate side-chains 156 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain A residue 36 ASP 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 Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 chunk 17 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 0.0070 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 overall best weight: 2.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7443 Z= 0.209 Angle : 0.666 9.004 10053 Z= 0.327 Chirality : 0.045 0.132 1125 Planarity : 0.004 0.042 1326 Dihedral : 6.006 22.817 1059 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 4.63 % Allowed : 18.02 % Favored : 77.35 % 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: -4.75 (0.24), residues: 942 helix: -4.76 (0.21), residues: 120 sheet: -3.07 (0.28), residues: 297 loop : -2.80 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 315 HIS 0.002 0.001 HIS A 246 PHE 0.011 0.001 PHE A 265 TYR 0.010 0.001 TYR B 216 ARG 0.008 0.000 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 159 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: C 209 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6440 (mtt) REVERT: B 120 ARG cc_start: 0.6901 (mtt180) cc_final: 0.6541 (mmt-90) REVERT: B 209 MET cc_start: 0.6591 (ptp) cc_final: 0.6296 (ptp) REVERT: B 294 LYS cc_start: 0.4643 (OUTLIER) cc_final: 0.4311 (mtpt) REVERT: B 310 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6442 (m-10) REVERT: A 215 ARG cc_start: 0.6619 (mtt180) cc_final: 0.5628 (mmm160) REVERT: A 259 LYS cc_start: 0.5904 (mttt) cc_final: 0.5471 (mmtp) outliers start: 36 outliers final: 27 residues processed: 143 average time/residue: 0.2593 time to fit residues: 46.3275 Evaluate side-chains 150 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 317 THR 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 42 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 0.0000 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 54 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 55 optimal weight: 0.0470 overall best weight: 4.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7443 Z= 0.276 Angle : 0.689 8.008 10053 Z= 0.343 Chirality : 0.045 0.133 1125 Planarity : 0.005 0.045 1326 Dihedral : 6.127 23.344 1059 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 5.92 % Allowed : 17.76 % Favored : 76.32 % 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: -4.77 (0.21), residues: 120 sheet: -3.12 (0.28), residues: 297 loop : -2.82 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 315 HIS 0.003 0.001 HIS A 246 PHE 0.011 0.001 PHE C 199 TYR 0.008 0.001 TYR C 310 ARG 0.012 0.000 ARG C 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 171 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 125 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7312 (mtt90) cc_final: 0.6886 (mtt180) REVERT: C 209 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6475 (mtt) REVERT: C 230 LYS cc_start: 0.3154 (mttt) cc_final: 0.2769 (tppp) REVERT: B 120 ARG cc_start: 0.6991 (mtt180) cc_final: 0.6533 (mpt-90) REVERT: B 157 ARG cc_start: 0.3951 (mmm160) cc_final: 0.3552 (mmm160) REVERT: B 169 MET cc_start: 0.3048 (mmt) cc_final: 0.2392 (mmt) REVERT: B 199 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6640 (m-80) REVERT: B 294 LYS cc_start: 0.4881 (OUTLIER) cc_final: 0.4553 (mtpt) REVERT: B 310 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6634 (m-10) REVERT: A 205 ASP cc_start: 0.7976 (m-30) cc_final: 0.7320 (m-30) REVERT: A 215 ARG cc_start: 0.6604 (mtt180) cc_final: 0.5579 (mmm160) REVERT: A 230 LYS cc_start: 0.3497 (mttt) cc_final: 0.3104 (tptp) REVERT: A 259 LYS cc_start: 0.5924 (mttt) cc_final: 0.5485 (mmtp) outliers start: 46 outliers final: 30 residues processed: 153 average time/residue: 0.2606 time to fit residues: 49.9946 Evaluate side-chains 159 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 209 MET Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 321 CYS 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 198 SER Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 294 LYS 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 317 THR Chi-restraints excluded: chain A residue 36 ASP 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 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 0.0040 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7443 Z= 0.158 Angle : 0.640 7.661 10053 Z= 0.315 Chirality : 0.044 0.131 1125 Planarity : 0.004 0.040 1326 Dihedral : 5.630 21.239 1059 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.32 % Allowed : 21.75 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.24), residues: 942 helix: -4.72 (0.23), residues: 120 sheet: -2.93 (0.28), residues: 312 loop : -2.75 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 82 HIS 0.002 0.001 HIS A 246 PHE 0.006 0.001 PHE C 265 TYR 0.004 0.001 TYR C 159 ARG 0.008 0.000 ARG C 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 146 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: C 120 ARG cc_start: 0.7219 (mtt90) cc_final: 0.6936 (mtt180) REVERT: B 120 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6436 (mpt-90) REVERT: B 169 MET cc_start: 0.2702 (mmt) cc_final: 0.2356 (mmt) REVERT: B 209 MET cc_start: 0.5622 (ptp) cc_final: 0.5295 (ptp) REVERT: B 300 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7784 (tp30) REVERT: B 310 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: A 205 ASP cc_start: 0.7826 (m-30) cc_final: 0.7126 (m-30) REVERT: A 215 ARG cc_start: 0.6514 (mtt180) cc_final: 0.5568 (mmm160) REVERT: A 230 LYS cc_start: 0.3001 (mttt) cc_final: 0.2513 (tppp) REVERT: A 259 LYS cc_start: 0.5960 (mttt) cc_final: 0.5446 (mmmt) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 0.2569 time to fit residues: 45.2055 Evaluate side-chains 135 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7443 Z= 0.246 Angle : 0.671 8.591 10053 Z= 0.331 Chirality : 0.044 0.141 1125 Planarity : 0.005 0.043 1326 Dihedral : 5.841 22.428 1059 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 3.35 % Allowed : 21.49 % Favored : 75.16 % 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: -4.59 (0.24), residues: 942 helix: -4.73 (0.23), residues: 120 sheet: -2.89 (0.29), residues: 297 loop : -2.73 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 315 HIS 0.003 0.001 HIS A 246 PHE 0.009 0.001 PHE C 199 TYR 0.007 0.001 TYR B 159 ARG 0.014 0.000 ARG B 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 150 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.825 Fit side-chains REVERT: C 120 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6983 (mtt180) REVERT: C 230 LYS cc_start: 0.2844 (mttt) cc_final: 0.2539 (tppp) REVERT: B 120 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6531 (mpt-90) REVERT: B 157 ARG cc_start: 0.3917 (mmm160) cc_final: 0.3199 (mmm160) REVERT: B 209 MET cc_start: 0.5781 (ptp) cc_final: 0.5488 (ptp) REVERT: B 300 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7391 (tp30) REVERT: B 310 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6597 (m-10) REVERT: A 205 ASP cc_start: 0.7974 (m-30) cc_final: 0.7315 (m-30) REVERT: A 215 ARG cc_start: 0.6647 (mtt180) cc_final: 0.5622 (mmm160) REVERT: A 230 LYS cc_start: 0.3464 (mttt) cc_final: 0.2852 (tppp) REVERT: A 259 LYS cc_start: 0.5980 (mttt) cc_final: 0.5451 (mmmt) outliers start: 26 outliers final: 21 residues processed: 139 average time/residue: 0.2596 time to fit residues: 45.4342 Evaluate side-chains 145 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain B residue 79 THR 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 317 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.0770 chunk 41 optimal weight: 40.0000 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5119 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= 0.197 Angle : 0.653 8.292 10053 Z= 0.321 Chirality : 0.044 0.135 1125 Planarity : 0.004 0.041 1326 Dihedral : 5.667 21.592 1059 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 2.83 % Allowed : 22.01 % Favored : 75.16 % 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: -4.52 (0.25), residues: 942 helix: -4.73 (0.22), residues: 120 sheet: -2.77 (0.28), residues: 315 loop : -2.69 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 315 HIS 0.002 0.001 HIS A 246 PHE 0.008 0.001 PHE C 199 TYR 0.007 0.001 TYR C 159 ARG 0.011 0.000 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 146 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.834 Fit side-chains REVERT: C 120 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6862 (mtt180) REVERT: B 157 ARG cc_start: 0.3809 (mmm160) cc_final: 0.3205 (mmm160) REVERT: B 169 MET cc_start: 0.2823 (mmt) cc_final: 0.2404 (mmt) REVERT: B 209 MET cc_start: 0.5878 (ptp) cc_final: 0.5597 (ptp) REVERT: B 300 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7462 (tp30) REVERT: B 310 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6459 (m-10) REVERT: A 157 ARG cc_start: 0.3883 (mmp80) cc_final: 0.3333 (mmm160) REVERT: A 205 ASP cc_start: 0.7870 (m-30) cc_final: 0.7222 (m-30) REVERT: A 230 LYS cc_start: 0.3223 (mttt) cc_final: 0.2647 (tppp) REVERT: A 259 LYS cc_start: 0.5972 (mttt) cc_final: 0.5478 (mmmt) outliers start: 22 outliers final: 20 residues processed: 139 average time/residue: 0.2512 time to fit residues: 43.9307 Evaluate side-chains 141 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 317 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 126 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.216011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.184561 restraints weight = 8071.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.183210 restraints weight = 12593.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.182407 restraints weight = 11383.307| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.5278 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= 0.260 Angle : 0.682 7.812 10053 Z= 0.338 Chirality : 0.045 0.223 1125 Planarity : 0.005 0.043 1326 Dihedral : 5.859 22.501 1059 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 3.47 % Allowed : 21.36 % Favored : 75.16 % 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: -4.54 (0.25), residues: 942 helix: -4.69 (0.24), residues: 123 sheet: -2.73 (0.29), residues: 309 loop : -2.74 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 315 HIS 0.003 0.001 HIS A 246 PHE 0.011 0.001 PHE C 199 TYR 0.007 0.001 TYR C 159 ARG 0.010 0.000 ARG B 157 =============================================================================== Job complete usr+sys time: 1779.19 seconds wall clock time: 32 minutes 54.72 seconds (1974.72 seconds total)