Starting phenix.real_space_refine on Sat Aug 23 05:56:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqd_34024/08_2025/7yqd_34024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqd_34024/08_2025/7yqd_34024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yqd_34024/08_2025/7yqd_34024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqd_34024/08_2025/7yqd_34024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqd_34024/08_2025/7yqd_34024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqd_34024/08_2025/7yqd_34024.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 28 5.16 5 C 6671 2.51 5 N 1771 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1470 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.71, per 1000 atoms: 0.17 Number of scatterers: 10290 At special positions: 0 Unit cell: (110.24, 112.32, 78, 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 28 16.00 O 1820 8.00 N 1771 7.00 C 6671 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: 1.03 Conformation dependent library (CDL) restraints added in 410.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE A 52 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 143 Proline residue: A 124 - end of helix removed outlier: 3.598A pdb=" N THR A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 244 removed outlier: 4.113A pdb=" N ARG A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE B 52 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 143 Proline residue: B 124 - end of helix removed outlier: 3.598A pdb=" N THR B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE C 52 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 143 Proline residue: C 124 - end of helix removed outlier: 3.598A pdb=" N THR C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 207 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 32 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 48 through 52 removed outlier: 4.075A pdb=" N ILE D 52 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 143 Proline residue: D 124 - end of helix removed outlier: 3.598A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 32 Processing helix chain 'E' and resid 32 through 47 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE E 52 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 143 Proline residue: E 124 - end of helix removed outlier: 3.598A pdb=" N THR E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 244 removed outlier: 4.113A pdb=" N ARG E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 207 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 32 Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE F 52 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 143 Proline residue: F 124 - end of helix removed outlier: 3.598A pdb=" N THR F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 196 removed outlier: 3.542A pdb=" N TYR F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 194 " --> pdb=" O VAL F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG F 203 " --> pdb=" O VAL F 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 207 " --> pdb=" O ARG F 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS F 241 " --> pdb=" O LYS F 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 32 Processing helix chain 'G' and resid 32 through 47 Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.074A pdb=" N ILE G 52 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 143 Proline residue: G 124 - end of helix removed outlier: 3.599A pdb=" N THR G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 196 removed outlier: 3.543A pdb=" N TYR G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 244 removed outlier: 4.112A pdb=" N ARG G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 207 " --> pdb=" O ARG G 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) 931 hydrogen bonds defined for protein. 2772 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: 1.65 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1938 1.33 - 1.45: 2164 1.45 - 1.57: 6272 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 10423 Sorted by residual: bond pdb=" N ILE F 144 " pdb=" CA ILE F 144 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N ILE C 144 " pdb=" CA ILE C 144 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.32e+01 bond pdb=" N ILE B 144 " pdb=" CA ILE B 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.29e+01 bond pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.28e+01 bond pdb=" N ILE E 144 " pdb=" CA ILE E 144 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.28e+01 ... (remaining 10418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8209 1.13 - 2.27: 3856 2.27 - 3.40: 1853 3.40 - 4.54: 168 4.54 - 5.67: 33 Bond angle restraints: 14119 Sorted by residual: angle pdb=" CA ILE D 144 " pdb=" C ILE D 144 " pdb=" N PRO D 145 " ideal model delta sigma weight residual 119.30 122.49 -3.19 8.10e-01 1.52e+00 1.55e+01 angle pdb=" CA ILE G 144 " pdb=" C ILE G 144 " pdb=" N PRO G 145 " ideal model delta sigma weight residual 119.30 122.48 -3.18 8.10e-01 1.52e+00 1.54e+01 angle pdb=" CA ILE A 144 " pdb=" C ILE A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 119.30 122.47 -3.17 8.10e-01 1.52e+00 1.53e+01 angle pdb=" CA ILE E 144 " pdb=" C ILE E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 119.30 122.46 -3.16 8.10e-01 1.52e+00 1.52e+01 angle pdb=" CA ILE F 144 " pdb=" C ILE F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 119.30 122.45 -3.15 8.10e-01 1.52e+00 1.52e+01 ... (remaining 14114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.67: 5559 11.67 - 23.35: 566 23.35 - 35.02: 189 35.02 - 46.69: 105 46.69 - 58.36: 49 Dihedral angle restraints: 6468 sinusoidal: 2464 harmonic: 4004 Sorted by residual: dihedral pdb=" C GLN A 178 " pdb=" N GLN A 178 " pdb=" CA GLN A 178 " pdb=" CB GLN A 178 " ideal model delta harmonic sigma weight residual -122.60 -133.35 10.75 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C GLN E 178 " pdb=" N GLN E 178 " pdb=" CA GLN E 178 " pdb=" CB GLN E 178 " ideal model delta harmonic sigma weight residual -122.60 -133.32 10.72 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C GLN B 178 " pdb=" N GLN B 178 " pdb=" CA GLN B 178 " pdb=" CB GLN B 178 " ideal model delta harmonic sigma weight residual -122.60 -133.31 10.71 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 6465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 684 0.067 - 0.134: 761 0.134 - 0.201: 277 0.201 - 0.268: 49 0.268 - 0.335: 7 Chirality restraints: 1778 Sorted by residual: chirality pdb=" CA GLN A 178 " pdb=" N GLN A 178 " pdb=" C GLN A 178 " pdb=" CB GLN A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA GLN D 178 " pdb=" N GLN D 178 " pdb=" C GLN D 178 " pdb=" CB GLN D 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA GLN E 178 " pdb=" N GLN E 178 " pdb=" C GLN E 178 " pdb=" CB GLN E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1775 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 120 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C GLU A 120 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU A 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 121 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 120 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLU G 120 " 0.023 2.00e-02 2.50e+03 pdb=" O GLU G 120 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS G 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 120 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C GLU C 120 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU C 120 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS C 121 " 0.008 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3223 2.85 - 3.36: 11277 3.36 - 3.87: 15518 3.87 - 4.39: 18213 4.39 - 4.90: 30412 Nonbonded interactions: 78643 Sorted by model distance: nonbonded pdb=" CB ASN F 226 " pdb=" CE MET G 138 " model vdw 2.335 3.860 nonbonded pdb=" CB ASN A 226 " pdb=" CE MET C 138 " model vdw 2.343 3.860 nonbonded pdb=" CB ASN C 226 " pdb=" CE MET D 138 " model vdw 2.349 3.860 nonbonded pdb=" CB ASN D 226 " pdb=" CE MET E 138 " model vdw 2.349 3.860 nonbonded pdb=" CE MET B 138 " pdb=" CB ASN G 226 " model vdw 2.352 3.860 ... (remaining 78638 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic 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: 1.270 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.012 0.038 10423 Z= 0.906 Angle : 1.460 5.669 14119 Z= 1.214 Chirality : 0.104 0.335 1778 Planarity : 0.005 0.022 1722 Dihedral : 13.548 58.363 3822 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 7.63 % Allowed : 7.92 % Favored : 84.45 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 6.20 (0.18), residues: 1288 helix: 4.77 (0.11), residues: 1092 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 204 TYR 0.010 0.002 TYR G 183 PHE 0.006 0.001 PHE G 44 TRP 0.010 0.002 TRP D 139 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.01154 (10423) covalent geometry : angle 1.45973 (14119) hydrogen bonds : bond 0.24418 ( 931) hydrogen bonds : angle 5.36735 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 372 time to evaluate : 0.470 Fit side-chains REVERT: A 54 ASP cc_start: 0.8387 (t0) cc_final: 0.7993 (t70) REVERT: A 238 ASN cc_start: 0.8511 (m-40) cc_final: 0.8253 (m-40) REVERT: B 37 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9240 (mmtt) REVERT: B 54 ASP cc_start: 0.8484 (t0) cc_final: 0.7906 (t0) REVERT: B 201 ASP cc_start: 0.7901 (m-30) cc_final: 0.7485 (m-30) REVERT: C 54 ASP cc_start: 0.8467 (t0) cc_final: 0.8071 (t0) REVERT: C 234 MET cc_start: 0.9020 (ttm) cc_final: 0.8798 (ttm) REVERT: D 37 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9150 (mmtt) REVERT: D 54 ASP cc_start: 0.8526 (t0) cc_final: 0.7974 (t0) REVERT: D 166 ARG cc_start: 0.8996 (ttp-170) cc_final: 0.8636 (mtt90) REVERT: E 54 ASP cc_start: 0.8478 (t0) cc_final: 0.8030 (t70) REVERT: F 54 ASP cc_start: 0.8476 (t0) cc_final: 0.8201 (t0) REVERT: G 54 ASP cc_start: 0.8449 (t0) cc_final: 0.8092 (t0) REVERT: G 117 ASP cc_start: 0.8424 (m-30) cc_final: 0.8016 (m-30) outliers start: 81 outliers final: 40 residues processed: 425 average time/residue: 0.1203 time to fit residues: 69.2301 Evaluate side-chains 359 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 112 ASN A 158 GLN A 178 GLN B 112 ASN B 178 GLN C 178 GLN D 178 GLN E 112 ASN E 178 GLN ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN G 178 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088939 restraints weight = 18500.278| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.65 r_work: 0.2956 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10423 Z= 0.187 Angle : 0.562 8.890 14119 Z= 0.308 Chirality : 0.037 0.132 1778 Planarity : 0.004 0.047 1722 Dihedral : 8.244 59.317 1498 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.94 % Allowed : 15.93 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.36 (0.19), residues: 1288 helix: 4.11 (0.12), residues: 1092 sheet: None (None), residues: 0 loop : -0.41 (0.28), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 21 TYR 0.018 0.001 TYR F 214 PHE 0.006 0.001 PHE E 33 TRP 0.002 0.000 TRP B 139 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00341 (10423) covalent geometry : angle 0.56249 (14119) hydrogen bonds : bond 0.08423 ( 931) hydrogen bonds : angle 3.83928 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 332 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8723 (t0) cc_final: 0.7991 (t70) REVERT: A 57 GLN cc_start: 0.8454 (mp10) cc_final: 0.7993 (mp10) REVERT: B 37 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.8985 (mmmt) REVERT: B 54 ASP cc_start: 0.8679 (t0) cc_final: 0.8013 (t70) REVERT: B 62 MET cc_start: 0.7038 (mtp) cc_final: 0.6720 (ttm) REVERT: B 128 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8383 (mm) REVERT: B 166 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8450 (ttp-170) REVERT: C 54 ASP cc_start: 0.8587 (t0) cc_final: 0.8011 (t0) REVERT: C 166 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8539 (ttp-170) REVERT: D 37 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8976 (mmtt) REVERT: D 54 ASP cc_start: 0.8746 (t0) cc_final: 0.8308 (t0) REVERT: D 166 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8609 (mtt90) REVERT: E 54 ASP cc_start: 0.8676 (t0) cc_final: 0.8040 (t0) REVERT: E 57 GLN cc_start: 0.8519 (mp10) cc_final: 0.8248 (mp10) REVERT: E 227 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8440 (mm-40) REVERT: F 54 ASP cc_start: 0.8648 (t0) cc_final: 0.8172 (t0) REVERT: F 57 GLN cc_start: 0.8599 (mp10) cc_final: 0.8333 (mp10) REVERT: F 166 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8610 (ttp-170) REVERT: F 203 ARG cc_start: 0.7518 (ttm110) cc_final: 0.7234 (mtp85) REVERT: G 54 ASP cc_start: 0.8606 (t0) cc_final: 0.7805 (t0) REVERT: G 57 GLN cc_start: 0.8536 (mp10) cc_final: 0.8146 (mp10) outliers start: 63 outliers final: 32 residues processed: 367 average time/residue: 0.1170 time to fit residues: 58.6664 Evaluate side-chains 341 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 166 ARG Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 178 GLN A 238 ASN B 178 GLN B 238 ASN C 112 ASN C 178 GLN D 178 GLN E 112 ASN E 178 GLN F 178 GLN F 226 ASN F 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088797 restraints weight = 18624.776| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.68 r_work: 0.2957 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10423 Z= 0.159 Angle : 0.483 6.796 14119 Z= 0.265 Chirality : 0.035 0.126 1778 Planarity : 0.004 0.029 1722 Dihedral : 6.095 57.018 1464 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.09 % Allowed : 18.76 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.10 (0.20), residues: 1288 helix: 3.91 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 21 TYR 0.012 0.001 TYR F 214 PHE 0.005 0.001 PHE E 18 TRP 0.004 0.000 TRP C 139 HIS 0.002 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00295 (10423) covalent geometry : angle 0.48280 (14119) hydrogen bonds : bond 0.07432 ( 931) hydrogen bonds : angle 3.59913 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8769 (t0) cc_final: 0.8031 (t0) REVERT: B 37 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9068 (mmtt) REVERT: B 54 ASP cc_start: 0.8668 (t0) cc_final: 0.7796 (t70) REVERT: B 166 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8528 (ttp-170) REVERT: B 210 ASP cc_start: 0.8688 (m-30) cc_final: 0.8377 (m-30) REVERT: C 54 ASP cc_start: 0.8607 (t0) cc_final: 0.8078 (t0) REVERT: C 142 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (mp) REVERT: C 166 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8697 (ttp-170) REVERT: D 37 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8799 (mmmt) REVERT: D 54 ASP cc_start: 0.8709 (t0) cc_final: 0.8167 (t0) REVERT: D 166 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8673 (mtt90) REVERT: D 188 LYS cc_start: 0.8835 (tttt) cc_final: 0.8458 (ttmm) REVERT: D 208 GLU cc_start: 0.8806 (tp30) cc_final: 0.8496 (tp30) REVERT: E 54 ASP cc_start: 0.8663 (t0) cc_final: 0.7939 (t0) REVERT: E 57 GLN cc_start: 0.8527 (mp10) cc_final: 0.8130 (mp10) REVERT: E 158 GLN cc_start: 0.8533 (tt0) cc_final: 0.8277 (tt0) REVERT: F 54 ASP cc_start: 0.8663 (t0) cc_final: 0.8269 (t0) REVERT: F 158 GLN cc_start: 0.8622 (tt0) cc_final: 0.8329 (tt0) REVERT: F 203 ARG cc_start: 0.7459 (ttm110) cc_final: 0.7220 (mtp85) REVERT: F 210 ASP cc_start: 0.8245 (m-30) cc_final: 0.7893 (m-30) REVERT: G 54 ASP cc_start: 0.8661 (t0) cc_final: 0.7838 (t0) REVERT: G 57 GLN cc_start: 0.8562 (mp10) cc_final: 0.8269 (mp10) outliers start: 54 outliers final: 37 residues processed: 350 average time/residue: 0.1179 time to fit residues: 56.2489 Evaluate side-chains 337 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 238 ASN B 112 ASN B 114 GLN B 178 GLN B 238 ASN C 112 ASN F 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088808 restraints weight = 18739.118| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.72 r_work: 0.2954 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10423 Z= 0.156 Angle : 0.485 6.057 14119 Z= 0.264 Chirality : 0.035 0.125 1778 Planarity : 0.004 0.027 1722 Dihedral : 6.070 56.521 1464 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.81 % Allowed : 19.89 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.91 (0.20), residues: 1288 helix: 3.76 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.29 (0.31), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 21 TYR 0.006 0.001 TYR F 214 PHE 0.005 0.001 PHE E 18 TRP 0.004 0.001 TRP E 139 HIS 0.001 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00306 (10423) covalent geometry : angle 0.48468 (14119) hydrogen bonds : bond 0.07032 ( 931) hydrogen bonds : angle 3.55454 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8708 (t0) cc_final: 0.8019 (t0) REVERT: A 142 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 37 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8898 (mmmt) REVERT: B 54 ASP cc_start: 0.8654 (t0) cc_final: 0.7840 (t70) REVERT: B 57 GLN cc_start: 0.8515 (mp10) cc_final: 0.8151 (mp10) REVERT: B 166 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8506 (ttp-170) REVERT: B 210 ASP cc_start: 0.8649 (m-30) cc_final: 0.8308 (m-30) REVERT: C 54 ASP cc_start: 0.8716 (t0) cc_final: 0.8261 (t70) REVERT: C 227 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8340 (mm-40) REVERT: D 37 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8798 (mmmt) REVERT: D 54 ASP cc_start: 0.8692 (t0) cc_final: 0.8071 (t0) REVERT: D 57 GLN cc_start: 0.8542 (mp10) cc_final: 0.8160 (mp10) REVERT: D 142 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 188 LYS cc_start: 0.8772 (tttt) cc_final: 0.8374 (ttmm) REVERT: D 208 GLU cc_start: 0.8826 (tp30) cc_final: 0.8484 (tp30) REVERT: E 54 ASP cc_start: 0.8672 (t0) cc_final: 0.8103 (t0) REVERT: E 57 GLN cc_start: 0.8569 (mp10) cc_final: 0.8360 (mp10) REVERT: F 54 ASP cc_start: 0.8682 (t0) cc_final: 0.8139 (t0) REVERT: F 210 ASP cc_start: 0.8288 (m-30) cc_final: 0.8028 (m-30) REVERT: G 54 ASP cc_start: 0.8694 (t0) cc_final: 0.7986 (t0) outliers start: 51 outliers final: 36 residues processed: 336 average time/residue: 0.1120 time to fit residues: 51.9499 Evaluate side-chains 332 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN D 178 GLN E 112 ASN E 178 GLN E 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089451 restraints weight = 18571.067| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.72 r_work: 0.2967 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10423 Z= 0.153 Angle : 0.495 7.743 14119 Z= 0.268 Chirality : 0.035 0.125 1778 Planarity : 0.004 0.032 1722 Dihedral : 5.892 55.868 1462 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 4.15 % Allowed : 19.98 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.85 (0.21), residues: 1288 helix: 3.72 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.29 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 21 TYR 0.005 0.001 TYR A 183 PHE 0.005 0.001 PHE E 18 TRP 0.004 0.001 TRP C 139 HIS 0.002 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00303 (10423) covalent geometry : angle 0.49465 (14119) hydrogen bonds : bond 0.06745 ( 931) hydrogen bonds : angle 3.50426 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8778 (t0) cc_final: 0.7837 (t0) REVERT: B 54 ASP cc_start: 0.8707 (t0) cc_final: 0.7969 (t70) REVERT: B 210 ASP cc_start: 0.8577 (m-30) cc_final: 0.8260 (m-30) REVERT: B 226 ASN cc_start: 0.7369 (t0) cc_final: 0.7035 (t0) REVERT: C 54 ASP cc_start: 0.8668 (t0) cc_final: 0.7936 (t0) REVERT: C 211 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8165 (tp30) REVERT: C 227 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8226 (mm-40) REVERT: D 37 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8744 (mmmt) REVERT: D 54 ASP cc_start: 0.8733 (t0) cc_final: 0.8251 (t0) REVERT: D 188 LYS cc_start: 0.8769 (tttt) cc_final: 0.8360 (ttmm) REVERT: D 208 GLU cc_start: 0.8852 (tp30) cc_final: 0.8486 (tp30) REVERT: E 54 ASP cc_start: 0.8662 (t0) cc_final: 0.8045 (t0) REVERT: E 57 GLN cc_start: 0.8618 (mp10) cc_final: 0.8315 (mp10) REVERT: E 62 MET cc_start: 0.7421 (mtp) cc_final: 0.7037 (ttm) REVERT: F 54 ASP cc_start: 0.8651 (t0) cc_final: 0.8224 (t70) REVERT: G 54 ASP cc_start: 0.8701 (t0) cc_final: 0.7853 (t0) REVERT: G 57 GLN cc_start: 0.8610 (mp10) cc_final: 0.8266 (mp10) outliers start: 44 outliers final: 32 residues processed: 327 average time/residue: 0.1123 time to fit residues: 50.6240 Evaluate side-chains 319 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN A 226 ASN A 238 ASN B 178 GLN B 238 ASN C 112 ASN C 178 GLN D 178 GLN D 226 ASN E 112 ASN E 178 GLN F 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.090981 restraints weight = 18658.829| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.76 r_work: 0.2996 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10423 Z= 0.144 Angle : 0.485 6.940 14119 Z= 0.263 Chirality : 0.035 0.124 1778 Planarity : 0.004 0.042 1722 Dihedral : 5.463 55.343 1454 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 4.43 % Allowed : 19.98 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.21), residues: 1288 helix: 3.73 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.25 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 21 TYR 0.004 0.001 TYR A 183 PHE 0.006 0.001 PHE E 18 TRP 0.007 0.001 TRP G 139 HIS 0.001 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00274 (10423) covalent geometry : angle 0.48471 (14119) hydrogen bonds : bond 0.06283 ( 931) hydrogen bonds : angle 3.43253 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8838 (t0) cc_final: 0.7995 (t0) REVERT: A 57 GLN cc_start: 0.8421 (mp10) cc_final: 0.7971 (mp10) REVERT: A 112 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8153 (t0) REVERT: A 211 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8305 (mm-30) REVERT: B 54 ASP cc_start: 0.8601 (t0) cc_final: 0.7936 (t70) REVERT: B 57 GLN cc_start: 0.8635 (mp10) cc_final: 0.8385 (mp10) REVERT: B 210 ASP cc_start: 0.8569 (m-30) cc_final: 0.8258 (m-30) REVERT: B 226 ASN cc_start: 0.7304 (t0) cc_final: 0.7026 (t0) REVERT: C 54 ASP cc_start: 0.8665 (t0) cc_final: 0.7970 (t0) REVERT: C 210 ASP cc_start: 0.8397 (m-30) cc_final: 0.8174 (m-30) REVERT: D 37 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8724 (mmmt) REVERT: D 54 ASP cc_start: 0.8673 (t0) cc_final: 0.8082 (t0) REVERT: D 57 GLN cc_start: 0.8495 (mp10) cc_final: 0.8133 (mp10) REVERT: D 188 LYS cc_start: 0.8736 (tttt) cc_final: 0.8319 (ttmm) REVERT: E 54 ASP cc_start: 0.8671 (t0) cc_final: 0.8020 (t0) REVERT: E 57 GLN cc_start: 0.8644 (mp10) cc_final: 0.8318 (mp10) REVERT: E 166 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8265 (ttp-170) REVERT: F 54 ASP cc_start: 0.8657 (t0) cc_final: 0.8070 (t70) REVERT: F 57 GLN cc_start: 0.8467 (mp10) cc_final: 0.8241 (mp10) REVERT: F 210 ASP cc_start: 0.8135 (m-30) cc_final: 0.7774 (m-30) REVERT: G 54 ASP cc_start: 0.8674 (t0) cc_final: 0.7824 (t0) REVERT: G 57 GLN cc_start: 0.8657 (mp10) cc_final: 0.8409 (mp10) REVERT: G 62 MET cc_start: 0.7216 (mtp) cc_final: 0.7006 (ttm) outliers start: 47 outliers final: 36 residues processed: 332 average time/residue: 0.1107 time to fit residues: 50.7368 Evaluate side-chains 313 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN A 238 ASN B 9 GLN B 178 GLN B 226 ASN B 238 ASN C 112 ASN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 178 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.090566 restraints weight = 18446.040| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.74 r_work: 0.2988 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10423 Z= 0.151 Angle : 0.500 6.361 14119 Z= 0.273 Chirality : 0.036 0.127 1778 Planarity : 0.004 0.043 1722 Dihedral : 5.428 55.041 1454 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 3.86 % Allowed : 20.74 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.21), residues: 1288 helix: 3.66 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 21 TYR 0.005 0.001 TYR D 214 PHE 0.006 0.001 PHE E 18 TRP 0.007 0.001 TRP G 139 HIS 0.001 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00304 (10423) covalent geometry : angle 0.50023 (14119) hydrogen bonds : bond 0.06296 ( 931) hydrogen bonds : angle 3.48231 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 280 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8777 (t0) cc_final: 0.8049 (t0) REVERT: A 211 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8304 (mm-30) REVERT: B 54 ASP cc_start: 0.8640 (t0) cc_final: 0.7942 (t70) REVERT: B 57 GLN cc_start: 0.8638 (mp10) cc_final: 0.8379 (mp10) REVERT: B 210 ASP cc_start: 0.8569 (m-30) cc_final: 0.8277 (m-30) REVERT: C 54 ASP cc_start: 0.8662 (t0) cc_final: 0.7839 (t0) REVERT: C 57 GLN cc_start: 0.8197 (mp10) cc_final: 0.7871 (mp10) REVERT: C 142 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8272 (mp) REVERT: C 210 ASP cc_start: 0.8327 (m-30) cc_final: 0.8105 (m-30) REVERT: D 37 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (mmmt) REVERT: D 54 ASP cc_start: 0.8615 (t0) cc_final: 0.7685 (t0) REVERT: D 57 GLN cc_start: 0.8519 (mp10) cc_final: 0.8051 (mp10) REVERT: D 188 LYS cc_start: 0.8740 (tttt) cc_final: 0.8330 (ttmm) REVERT: E 54 ASP cc_start: 0.8692 (t0) cc_final: 0.7396 (t0) REVERT: E 57 GLN cc_start: 0.8649 (mp10) cc_final: 0.8019 (mp10) REVERT: E 166 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8285 (ttp-170) REVERT: F 54 ASP cc_start: 0.8695 (t0) cc_final: 0.8317 (t70) REVERT: F 210 ASP cc_start: 0.8271 (m-30) cc_final: 0.8022 (m-30) REVERT: G 54 ASP cc_start: 0.8655 (t0) cc_final: 0.7784 (t0) REVERT: G 57 GLN cc_start: 0.8657 (mp10) cc_final: 0.8395 (mp10) REVERT: G 62 MET cc_start: 0.7347 (mtp) cc_final: 0.7094 (ttm) outliers start: 41 outliers final: 31 residues processed: 314 average time/residue: 0.1089 time to fit residues: 47.4021 Evaluate side-chains 307 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 GLN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 178 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 178 GLN B 238 ASN C 178 GLN D 178 GLN E 178 GLN E 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091874 restraints weight = 18671.075| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.78 r_work: 0.3006 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10423 Z= 0.144 Angle : 0.513 10.933 14119 Z= 0.275 Chirality : 0.036 0.179 1778 Planarity : 0.004 0.051 1722 Dihedral : 5.172 55.281 1449 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.68 % Allowed : 21.21 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.72 (0.21), residues: 1288 helix: 3.64 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.38 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 21 TYR 0.004 0.001 TYR E 183 PHE 0.006 0.001 PHE E 18 TRP 0.010 0.001 TRP F 139 HIS 0.001 0.000 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00281 (10423) covalent geometry : angle 0.51337 (14119) hydrogen bonds : bond 0.06019 ( 931) hydrogen bonds : angle 3.44630 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8754 (t0) cc_final: 0.7797 (t0) REVERT: A 57 GLN cc_start: 0.8329 (mp10) cc_final: 0.7936 (mp10) REVERT: A 211 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8346 (mm-30) REVERT: B 54 ASP cc_start: 0.8561 (t0) cc_final: 0.7718 (t70) REVERT: B 57 GLN cc_start: 0.8589 (mp10) cc_final: 0.8146 (mp10) REVERT: B 210 ASP cc_start: 0.8571 (m-30) cc_final: 0.8309 (m-30) REVERT: C 54 ASP cc_start: 0.8706 (t0) cc_final: 0.8052 (t0) REVERT: C 210 ASP cc_start: 0.8325 (m-30) cc_final: 0.8081 (m-30) REVERT: D 37 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8725 (mmmt) REVERT: D 54 ASP cc_start: 0.8588 (t0) cc_final: 0.8099 (t0) REVERT: D 57 GLN cc_start: 0.8520 (mp10) cc_final: 0.8190 (mp10) REVERT: D 188 LYS cc_start: 0.8726 (tttt) cc_final: 0.8307 (ttmm) REVERT: E 54 ASP cc_start: 0.8679 (t0) cc_final: 0.7381 (t0) REVERT: E 57 GLN cc_start: 0.8654 (mp10) cc_final: 0.8015 (mp10) REVERT: E 166 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8264 (ttp-170) REVERT: F 54 ASP cc_start: 0.8666 (t0) cc_final: 0.8052 (t70) REVERT: F 210 ASP cc_start: 0.8298 (m-30) cc_final: 0.8092 (m-30) REVERT: G 54 ASP cc_start: 0.8644 (t0) cc_final: 0.7831 (t0) REVERT: G 57 GLN cc_start: 0.8715 (mp10) cc_final: 0.8467 (mp10) REVERT: G 62 MET cc_start: 0.7380 (mtp) cc_final: 0.7107 (ttm) outliers start: 39 outliers final: 30 residues processed: 321 average time/residue: 0.1095 time to fit residues: 48.9753 Evaluate side-chains 311 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 238 ASN D 112 ASN D 226 ASN E 178 GLN E 226 ASN E 238 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.090145 restraints weight = 18397.907| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.72 r_work: 0.2982 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10423 Z= 0.158 Angle : 0.555 14.471 14119 Z= 0.294 Chirality : 0.037 0.172 1778 Planarity : 0.004 0.051 1722 Dihedral : 5.161 54.709 1448 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.02 % Allowed : 21.77 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.58 (0.21), residues: 1288 helix: 3.56 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.51 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 21 TYR 0.005 0.001 TYR B 175 PHE 0.006 0.001 PHE E 18 TRP 0.008 0.001 TRP F 139 HIS 0.002 0.000 HIS G 53 Details of bonding type rmsd covalent geometry : bond 0.00332 (10423) covalent geometry : angle 0.55539 (14119) hydrogen bonds : bond 0.06278 ( 931) hydrogen bonds : angle 3.51107 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8735 (t0) cc_final: 0.7779 (t0) REVERT: A 57 GLN cc_start: 0.8384 (mp10) cc_final: 0.8003 (mp10) REVERT: A 211 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 54 ASP cc_start: 0.8626 (t0) cc_final: 0.7834 (t0) REVERT: B 57 GLN cc_start: 0.8594 (mp10) cc_final: 0.8236 (mp10) REVERT: B 210 ASP cc_start: 0.8618 (m-30) cc_final: 0.8345 (m-30) REVERT: C 54 ASP cc_start: 0.8737 (t0) cc_final: 0.7966 (t0) REVERT: C 57 GLN cc_start: 0.8182 (mp10) cc_final: 0.7945 (mp10) REVERT: C 210 ASP cc_start: 0.8348 (m-30) cc_final: 0.8099 (m-30) REVERT: D 37 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8754 (mmmt) REVERT: D 54 ASP cc_start: 0.8598 (t0) cc_final: 0.8081 (t0) REVERT: D 57 GLN cc_start: 0.8514 (mp10) cc_final: 0.8183 (mp10) REVERT: D 188 LYS cc_start: 0.8754 (tttt) cc_final: 0.8340 (ttmm) REVERT: E 54 ASP cc_start: 0.8698 (t0) cc_final: 0.7406 (t0) REVERT: E 57 GLN cc_start: 0.8650 (mp10) cc_final: 0.8009 (mp10) REVERT: E 166 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8272 (ttp-170) REVERT: F 54 ASP cc_start: 0.8686 (t0) cc_final: 0.7901 (t70) REVERT: F 57 GLN cc_start: 0.8558 (mp10) cc_final: 0.8233 (mp10) REVERT: G 54 ASP cc_start: 0.8605 (t0) cc_final: 0.7850 (t0) REVERT: G 57 GLN cc_start: 0.8686 (mp10) cc_final: 0.8476 (mp10) REVERT: G 62 MET cc_start: 0.7432 (mtp) cc_final: 0.7157 (ttm) outliers start: 32 outliers final: 27 residues processed: 310 average time/residue: 0.1164 time to fit residues: 49.4927 Evaluate side-chains 299 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 112 ASN B 178 GLN B 238 ASN C 178 GLN D 178 GLN E 178 GLN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091005 restraints weight = 18342.196| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.71 r_work: 0.2995 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10423 Z= 0.151 Angle : 0.542 11.990 14119 Z= 0.288 Chirality : 0.036 0.166 1778 Planarity : 0.004 0.052 1722 Dihedral : 5.016 54.742 1446 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.11 % Allowed : 21.58 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.61 (0.21), residues: 1288 helix: 3.58 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 21 TYR 0.006 0.001 TYR E 175 PHE 0.006 0.001 PHE E 18 TRP 0.008 0.001 TRP F 139 HIS 0.001 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00304 (10423) covalent geometry : angle 0.54161 (14119) hydrogen bonds : bond 0.06147 ( 931) hydrogen bonds : angle 3.51258 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.467 Fit side-chains REVERT: A 54 ASP cc_start: 0.8703 (t0) cc_final: 0.7709 (t0) REVERT: A 57 GLN cc_start: 0.8364 (mp10) cc_final: 0.8020 (mp10) REVERT: A 211 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8361 (mm-30) REVERT: B 54 ASP cc_start: 0.8611 (t0) cc_final: 0.7798 (t70) REVERT: B 57 GLN cc_start: 0.8653 (mp10) cc_final: 0.8286 (mp10) REVERT: B 210 ASP cc_start: 0.8637 (m-30) cc_final: 0.8418 (m-30) REVERT: C 54 ASP cc_start: 0.8750 (t0) cc_final: 0.8010 (t0) REVERT: C 57 GLN cc_start: 0.8147 (mp10) cc_final: 0.7915 (mp10) REVERT: C 188 LYS cc_start: 0.9330 (ttmm) cc_final: 0.8978 (tttt) REVERT: D 37 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8751 (mmmt) REVERT: D 54 ASP cc_start: 0.8564 (t0) cc_final: 0.8051 (t0) REVERT: D 57 GLN cc_start: 0.8506 (mp10) cc_final: 0.8183 (mp10) REVERT: D 188 LYS cc_start: 0.8715 (tttt) cc_final: 0.8302 (ttmm) REVERT: E 54 ASP cc_start: 0.8702 (t0) cc_final: 0.7412 (t0) REVERT: E 57 GLN cc_start: 0.8658 (mp10) cc_final: 0.8024 (mp10) REVERT: E 166 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8241 (ttp-170) REVERT: E 209 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7678 (tp) REVERT: F 54 ASP cc_start: 0.8695 (t0) cc_final: 0.7903 (t70) REVERT: F 57 GLN cc_start: 0.8540 (mp10) cc_final: 0.8207 (mp10) REVERT: G 54 ASP cc_start: 0.8657 (t0) cc_final: 0.7893 (t0) REVERT: G 62 MET cc_start: 0.7411 (mtp) cc_final: 0.7092 (ttm) outliers start: 33 outliers final: 28 residues processed: 307 average time/residue: 0.1114 time to fit residues: 47.1872 Evaluate side-chains 304 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 72 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 ASN B 178 GLN B 238 ASN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090840 restraints weight = 18546.760| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.73 r_work: 0.2991 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 10423 Z= 0.311 Angle : 1.416 59.200 14119 Z= 0.924 Chirality : 0.050 0.705 1778 Planarity : 0.007 0.143 1722 Dihedral : 5.275 54.735 1445 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.02 % Allowed : 22.05 % Favored : 74.93 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.51 (0.21), residues: 1288 helix: 3.51 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.53 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 21 TYR 0.005 0.001 TYR E 175 PHE 0.006 0.001 PHE E 18 TRP 0.007 0.001 TRP F 139 HIS 0.001 0.000 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00616 (10423) covalent geometry : angle 1.41561 (14119) hydrogen bonds : bond 0.06334 ( 931) hydrogen bonds : angle 3.61110 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.43 seconds wall clock time: 39 minutes 6.67 seconds (2346.67 seconds total)