Starting phenix.real_space_refine on Fri Feb 14 10:58:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqd_34024/02_2025/7yqd_34024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqd_34024/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqd_34024/02_2025/7yqd_34024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqd_34024/02_2025/7yqd_34024.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqd_34024/02_2025/7yqd_34024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqd_34024/02_2025/7yqd_34024.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.75, per 1000 atoms: 0.36 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.72 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: 2.87 Time building geometry restraints manager: 3.29 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: 0.01 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.360 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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= 0.762 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.010 0.002 TRP D 139 HIS 0.003 0.001 HIS E 232 PHE 0.006 0.001 PHE G 44 TYR 0.010 0.002 TYR G 183 ARG 0.002 0.001 ARG F 204 *********************** 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 : 1.229 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: 0.2519 time to fit residues: 143.5090 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 : 1.616 ------------------------------------------------------------------------------- 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 112 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 112 ASN A 158 GLN A 178 GLN B 112 ASN B 178 GLN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.109880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089050 restraints weight = 18393.278| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.63 r_work: 0.2960 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10423 Z= 0.211 Angle : 0.540 8.802 14119 Z= 0.297 Chirality : 0.036 0.133 1778 Planarity : 0.004 0.043 1722 Dihedral : 8.186 58.968 1498 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.84 % Allowed : 15.27 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.48 (0.19), residues: 1288 helix: 4.19 (0.12), residues: 1092 sheet: None (None), residues: 0 loop : -0.36 (0.28), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 139 HIS 0.003 0.001 HIS F 59 PHE 0.006 0.001 PHE A 18 TYR 0.017 0.001 TYR F 214 ARG 0.004 0.001 ARG D 21 *********************** 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 396 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8714 (t0) cc_final: 0.8157 (t70) REVERT: A 57 GLN cc_start: 0.8427 (mp10) cc_final: 0.8071 (mp10) REVERT: B 37 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9090 (mmtt) REVERT: B 54 ASP cc_start: 0.8678 (t0) cc_final: 0.8001 (t70) REVERT: B 62 MET cc_start: 0.7055 (mtp) cc_final: 0.6678 (ttm) REVERT: B 128 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 166 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8443 (ttp-170) REVERT: C 54 ASP cc_start: 0.8551 (t0) cc_final: 0.7960 (t0) REVERT: C 166 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8536 (ttp-170) REVERT: C 234 MET cc_start: 0.9205 (ttm) cc_final: 0.8831 (tmm) REVERT: D 37 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8948 (mmtt) REVERT: D 54 ASP cc_start: 0.8720 (t0) cc_final: 0.8289 (t0) REVERT: D 166 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8603 (mtt90) REVERT: E 54 ASP cc_start: 0.8661 (t0) cc_final: 0.8052 (t0) REVERT: E 57 GLN cc_start: 0.8494 (mp10) cc_final: 0.8219 (mp10) REVERT: F 54 ASP cc_start: 0.8642 (t0) cc_final: 0.8157 (t0) REVERT: F 57 GLN cc_start: 0.8551 (mp10) cc_final: 0.8256 (mp10) REVERT: F 166 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8600 (ttp-170) REVERT: F 203 ARG cc_start: 0.7503 (ttm110) cc_final: 0.7259 (mtp85) REVERT: F 210 ASP cc_start: 0.8370 (m-30) cc_final: 0.7981 (m-30) REVERT: G 54 ASP cc_start: 0.8651 (t0) cc_final: 0.7983 (t0) outliers start: 62 outliers final: 32 residues processed: 368 average time/residue: 0.2361 time to fit residues: 118.3002 Evaluate side-chains 339 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 45 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 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 66 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 238 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089437 restraints weight = 18662.754| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.68 r_work: 0.2966 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3971 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= 0.188 Angle : 0.481 6.644 14119 Z= 0.264 Chirality : 0.035 0.125 1778 Planarity : 0.004 0.029 1722 Dihedral : 6.111 57.292 1464 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.18 % Allowed : 18.38 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.16 (0.20), residues: 1288 helix: 3.95 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.33 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 139 HIS 0.002 0.000 HIS F 59 PHE 0.005 0.001 PHE E 18 TYR 0.012 0.001 TYR F 214 ARG 0.007 0.001 ARG G 21 *********************** 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 372 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 317 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8742 (t0) cc_final: 0.8154 (t70) REVERT: A 166 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8534 (ttp-110) REVERT: B 54 ASP cc_start: 0.8635 (t0) cc_final: 0.7780 (t70) REVERT: B 166 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8530 (ttp-170) REVERT: B 210 ASP cc_start: 0.8657 (m-30) cc_final: 0.8349 (m-30) REVERT: C 54 ASP cc_start: 0.8572 (t0) cc_final: 0.8019 (t0) REVERT: C 138 MET cc_start: 0.8395 (tpp) cc_final: 0.8005 (tpp) REVERT: C 142 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8457 (mp) REVERT: C 166 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8699 (ttp-170) REVERT: D 37 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8704 (mmmt) REVERT: D 54 ASP cc_start: 0.8692 (t0) cc_final: 0.8017 (t0) REVERT: D 57 GLN cc_start: 0.8468 (mp10) cc_final: 0.8099 (mp10) REVERT: D 166 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8703 (mtt90) REVERT: D 188 LYS cc_start: 0.8822 (tttt) cc_final: 0.8469 (ttmm) REVERT: D 208 GLU cc_start: 0.8787 (tp30) cc_final: 0.8481 (tp30) REVERT: E 54 ASP cc_start: 0.8660 (t0) cc_final: 0.7968 (t0) REVERT: E 57 GLN cc_start: 0.8539 (mp10) cc_final: 0.8153 (mp10) REVERT: E 158 GLN cc_start: 0.8533 (tt0) cc_final: 0.8282 (tt0) REVERT: F 54 ASP cc_start: 0.8643 (t0) cc_final: 0.8096 (t0) REVERT: F 203 ARG cc_start: 0.7449 (ttm110) cc_final: 0.7229 (mtp85) REVERT: F 210 ASP cc_start: 0.8232 (m-30) cc_final: 0.7894 (m-30) REVERT: G 54 ASP cc_start: 0.8562 (t0) cc_final: 0.7913 (t0) outliers start: 55 outliers final: 37 residues processed: 351 average time/residue: 0.2408 time to fit residues: 114.8594 Evaluate side-chains 339 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE 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 45 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 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 98 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 238 ASN B 112 ASN B 178 GLN B 238 ASN C 112 ASN E 112 ASN E 178 GLN E 238 ASN F 178 GLN F 226 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.090708 restraints weight = 18413.306| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.70 r_work: 0.2990 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4304 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= 0.178 Angle : 0.474 6.090 14119 Z= 0.259 Chirality : 0.035 0.122 1778 Planarity : 0.003 0.027 1722 Dihedral : 5.755 56.449 1458 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.90 % Allowed : 19.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.00 (0.20), residues: 1288 helix: 3.82 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.21 (0.31), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 139 HIS 0.002 0.000 HIS D 59 PHE 0.005 0.001 PHE E 18 TYR 0.007 0.001 TYR F 214 ARG 0.009 0.001 ARG B 21 *********************** 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 356 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8724 (t0) cc_final: 0.8076 (t0) REVERT: A 210 ASP cc_start: 0.8375 (m-30) cc_final: 0.8154 (m-30) REVERT: B 54 ASP cc_start: 0.8566 (t0) cc_final: 0.7779 (t70) REVERT: B 57 GLN cc_start: 0.8506 (mp10) cc_final: 0.8141 (mp10) REVERT: B 166 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8630 (mtt90) REVERT: B 210 ASP cc_start: 0.8680 (m-30) cc_final: 0.8360 (m-30) REVERT: C 54 ASP cc_start: 0.8669 (t0) cc_final: 0.8049 (t0) REVERT: D 37 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8673 (mmmt) REVERT: D 54 ASP cc_start: 0.8699 (t0) cc_final: 0.8218 (t0) REVERT: D 188 LYS cc_start: 0.8765 (tttt) cc_final: 0.8366 (ttmm) REVERT: D 208 GLU cc_start: 0.8811 (tp30) cc_final: 0.8475 (tp30) REVERT: E 54 ASP cc_start: 0.8636 (t0) cc_final: 0.8114 (t0) REVERT: F 54 ASP cc_start: 0.8605 (t0) cc_final: 0.8170 (t0) REVERT: F 109 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6123 (mp) REVERT: F 166 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8225 (mtt90) REVERT: G 54 ASP cc_start: 0.8568 (t0) cc_final: 0.8081 (t0) outliers start: 52 outliers final: 32 residues processed: 338 average time/residue: 0.2347 time to fit residues: 108.9166 Evaluate side-chains 328 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 293 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 239 ILE 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 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 155 VAL 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 109 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN B 114 GLN C 112 ASN C 178 GLN D 178 GLN E 238 ASN G 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090167 restraints weight = 18480.594| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.72 r_work: 0.2980 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4489 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= 0.198 Angle : 0.492 6.970 14119 Z= 0.266 Chirality : 0.035 0.132 1778 Planarity : 0.004 0.036 1722 Dihedral : 5.731 55.817 1458 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 4.05 % Allowed : 19.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.21), residues: 1288 helix: 3.74 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.24 (0.31), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 139 HIS 0.001 0.000 HIS D 59 PHE 0.005 0.001 PHE E 18 TYR 0.005 0.001 TYR G 183 ARG 0.010 0.001 ARG B 21 *********************** 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: 43 poor density : 295 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8748 (t0) cc_final: 0.8148 (t0) REVERT: B 54 ASP cc_start: 0.8639 (t0) cc_final: 0.7892 (t70) REVERT: B 210 ASP cc_start: 0.8563 (m-30) cc_final: 0.8251 (m-30) REVERT: C 54 ASP cc_start: 0.8667 (t0) cc_final: 0.8055 (t0) REVERT: C 142 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8474 (mp) REVERT: D 37 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8725 (mmmt) REVERT: D 54 ASP cc_start: 0.8655 (t0) cc_final: 0.8065 (t0) REVERT: D 57 GLN cc_start: 0.8501 (mp10) cc_final: 0.8108 (mp10) REVERT: D 142 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8421 (mp) REVERT: D 188 LYS cc_start: 0.8771 (tttt) cc_final: 0.8355 (ttmm) REVERT: D 208 GLU cc_start: 0.8817 (tp30) cc_final: 0.8466 (tp30) REVERT: E 54 ASP cc_start: 0.8614 (t0) cc_final: 0.8245 (t0) REVERT: E 62 MET cc_start: 0.7498 (mtp) cc_final: 0.7138 (ttm) REVERT: E 227 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8316 (mm-40) REVERT: F 54 ASP cc_start: 0.8649 (t0) cc_final: 0.8268 (t0) REVERT: F 109 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6225 (mp) REVERT: F 166 ARG cc_start: 0.8582 (ttp-170) cc_final: 0.8065 (mtm-85) REVERT: G 54 ASP cc_start: 0.8570 (t0) cc_final: 0.7854 (t0) REVERT: G 62 MET cc_start: 0.7292 (mtp) cc_final: 0.7055 (ttm) outliers start: 43 outliers final: 34 residues processed: 324 average time/residue: 0.2451 time to fit residues: 109.7031 Evaluate side-chains 320 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 142 LEU 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 52 ILE Chi-restraints excluded: chain E residue 56 THR 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 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 109 LEU 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 58 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 83 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 226 ASN A 238 ASN B 112 ASN B 226 ASN B 238 ASN C 112 ASN C 178 GLN C 226 ASN D 226 ASN E 112 ASN E 238 ASN F 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.091443 restraints weight = 18484.988| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.73 r_work: 0.3001 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10423 Z= 0.182 Angle : 0.496 7.280 14119 Z= 0.268 Chirality : 0.035 0.128 1778 Planarity : 0.004 0.039 1722 Dihedral : 5.509 55.906 1454 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 3.77 % Allowed : 20.45 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.21), residues: 1288 helix: 3.71 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.24 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 139 HIS 0.001 0.000 HIS C 53 PHE 0.005 0.001 PHE E 18 TYR 0.004 0.001 TYR B 183 ARG 0.013 0.001 ARG B 21 *********************** 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 332 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8808 (t0) cc_final: 0.7671 (t0) REVERT: A 57 GLN cc_start: 0.8443 (mp10) cc_final: 0.7804 (mp10) REVERT: A 210 ASP cc_start: 0.8342 (m-30) cc_final: 0.8117 (m-30) REVERT: B 54 ASP cc_start: 0.8570 (t0) cc_final: 0.7898 (t70) REVERT: B 57 GLN cc_start: 0.8598 (mp10) cc_final: 0.8357 (mp10) REVERT: B 210 ASP cc_start: 0.8512 (m-30) cc_final: 0.8223 (m-30) REVERT: C 54 ASP cc_start: 0.8580 (t0) cc_final: 0.7930 (t0) REVERT: C 138 MET cc_start: 0.9259 (tpt) cc_final: 0.9052 (tpt) REVERT: C 142 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8500 (mp) REVERT: C 210 ASP cc_start: 0.8414 (m-30) cc_final: 0.8166 (m-30) REVERT: D 37 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8731 (mmmt) REVERT: D 54 ASP cc_start: 0.8675 (t0) cc_final: 0.8221 (t0) REVERT: D 142 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 188 LYS cc_start: 0.8765 (tttt) cc_final: 0.8360 (ttmm) REVERT: E 54 ASP cc_start: 0.8572 (t0) cc_final: 0.8191 (t0) REVERT: F 54 ASP cc_start: 0.8598 (t0) cc_final: 0.8015 (t0) REVERT: F 57 GLN cc_start: 0.8419 (mp10) cc_final: 0.8219 (mp10) REVERT: F 62 MET cc_start: 0.7449 (mtp) cc_final: 0.7234 (mtp) REVERT: F 226 ASN cc_start: 0.8335 (m-40) cc_final: 0.8012 (m110) REVERT: G 54 ASP cc_start: 0.8569 (t0) cc_final: 0.7710 (t0) REVERT: G 57 GLN cc_start: 0.8578 (mp10) cc_final: 0.8178 (mp10) REVERT: G 62 MET cc_start: 0.7278 (mtp) cc_final: 0.7031 (ttm) outliers start: 40 outliers final: 33 residues processed: 323 average time/residue: 0.2297 time to fit residues: 102.6605 Evaluate side-chains 314 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 142 LEU 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 112 ASN Chi-restraints excluded: chain E residue 142 LEU 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 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 58 ILE Chi-restraints excluded: chain G residue 142 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 112 ASN B 238 ASN C 112 ASN D 178 GLN E 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091947 restraints weight = 18605.870| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.73 r_work: 0.3012 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4851 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= 0.183 Angle : 0.501 5.964 14119 Z= 0.271 Chirality : 0.035 0.129 1778 Planarity : 0.004 0.044 1722 Dihedral : 5.374 55.780 1452 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.96 % Allowed : 20.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.80 (0.21), residues: 1288 helix: 3.69 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.29 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 139 HIS 0.001 0.000 HIS D 59 PHE 0.005 0.001 PHE E 18 TYR 0.004 0.001 TYR A 183 ARG 0.014 0.001 ARG B 21 *********************** 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 323 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 281 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8803 (t0) cc_final: 0.7847 (t0) REVERT: A 57 GLN cc_start: 0.8429 (mp10) cc_final: 0.7965 (mp10) REVERT: B 54 ASP cc_start: 0.8579 (t0) cc_final: 0.7899 (t70) REVERT: B 57 GLN cc_start: 0.8629 (mp10) cc_final: 0.8392 (mp10) REVERT: B 210 ASP cc_start: 0.8483 (m-30) cc_final: 0.8254 (m-30) REVERT: C 54 ASP cc_start: 0.8579 (t0) cc_final: 0.7671 (t0) REVERT: C 57 GLN cc_start: 0.8136 (mp10) cc_final: 0.7823 (mp10) REVERT: C 142 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8215 (mp) REVERT: C 211 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: D 37 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8744 (mmmt) REVERT: D 54 ASP cc_start: 0.8646 (t0) cc_final: 0.8084 (t0) REVERT: D 57 GLN cc_start: 0.8479 (mp10) cc_final: 0.8173 (mp10) REVERT: D 142 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8374 (mp) REVERT: D 188 LYS cc_start: 0.8761 (tttt) cc_final: 0.8353 (ttmm) REVERT: E 54 ASP cc_start: 0.8590 (t0) cc_final: 0.8048 (t0) REVERT: E 57 GLN cc_start: 0.8627 (mp10) cc_final: 0.8246 (mp10) REVERT: F 54 ASP cc_start: 0.8622 (t0) cc_final: 0.8029 (t0) REVERT: F 62 MET cc_start: 0.7576 (mtp) cc_final: 0.7281 (mtp) REVERT: G 54 ASP cc_start: 0.8631 (t0) cc_final: 0.7829 (t0) REVERT: G 57 GLN cc_start: 0.8536 (mp10) cc_final: 0.8189 (mp10) REVERT: G 62 MET cc_start: 0.7307 (mtp) cc_final: 0.7053 (ttm) REVERT: G 138 MET cc_start: 0.9401 (tpt) cc_final: 0.9145 (mmm) outliers start: 42 outliers final: 33 residues processed: 314 average time/residue: 0.2315 time to fit residues: 100.3118 Evaluate side-chains 308 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 211 GLU 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 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 112 ASN Chi-restraints excluded: chain E residue 142 LEU 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 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 58 ILE Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 55 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 238 ASN C 178 GLN D 178 GLN E 112 ASN E 226 ASN E 238 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 = 0.3480 r_free = 0.3480 target = 0.114566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092360 restraints weight = 18492.738| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.74 r_work: 0.3013 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4983 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= 0.184 Angle : 0.529 12.712 14119 Z= 0.278 Chirality : 0.035 0.131 1778 Planarity : 0.004 0.047 1722 Dihedral : 5.222 55.867 1450 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 4.15 % Allowed : 20.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.80 (0.21), residues: 1288 helix: 3.69 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.32 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 139 HIS 0.001 0.000 HIS D 53 PHE 0.005 0.001 PHE E 18 TYR 0.004 0.001 TYR G 183 ARG 0.015 0.001 ARG B 21 *********************** 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 326 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8726 (t0) cc_final: 0.7653 (t0) REVERT: A 57 GLN cc_start: 0.8403 (mp10) cc_final: 0.7839 (mp10) REVERT: B 54 ASP cc_start: 0.8614 (t0) cc_final: 0.7963 (t70) REVERT: B 57 GLN cc_start: 0.8602 (mp10) cc_final: 0.8327 (mp10) REVERT: B 208 GLU cc_start: 0.8672 (tp30) cc_final: 0.8469 (tp30) REVERT: B 210 ASP cc_start: 0.8564 (m-30) cc_final: 0.8309 (m-30) REVERT: C 54 ASP cc_start: 0.8651 (t0) cc_final: 0.7725 (t0) REVERT: C 57 GLN cc_start: 0.8105 (mp10) cc_final: 0.7796 (mp10) REVERT: C 142 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 211 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: D 37 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8740 (mmmt) REVERT: D 54 ASP cc_start: 0.8602 (t0) cc_final: 0.8022 (t0) REVERT: D 57 GLN cc_start: 0.8512 (mp10) cc_final: 0.8171 (mp10) REVERT: D 188 LYS cc_start: 0.8733 (tttt) cc_final: 0.8312 (ttmm) REVERT: E 54 ASP cc_start: 0.8659 (t0) cc_final: 0.8060 (t0) REVERT: E 57 GLN cc_start: 0.8648 (mp10) cc_final: 0.8284 (mp10) REVERT: F 54 ASP cc_start: 0.8536 (t0) cc_final: 0.7916 (t70) REVERT: F 62 MET cc_start: 0.7563 (mtp) cc_final: 0.7281 (mtp) REVERT: G 54 ASP cc_start: 0.8630 (t0) cc_final: 0.7817 (t0) REVERT: G 57 GLN cc_start: 0.8544 (mp10) cc_final: 0.8170 (mp10) REVERT: G 62 MET cc_start: 0.7335 (mtp) cc_final: 0.7066 (ttm) outliers start: 44 outliers final: 33 residues processed: 318 average time/residue: 0.2436 time to fit residues: 109.4664 Evaluate side-chains 309 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 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 178 GLN Chi-restraints excluded: chain C residue 211 GLU 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 112 ASN Chi-restraints excluded: chain E residue 142 LEU 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 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 58 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 9 GLN B 112 ASN B 178 GLN B 238 ASN C 178 GLN D 178 GLN ** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091877 restraints weight = 18537.068| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.75 r_work: 0.3009 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10423 Z= 0.194 Angle : 0.559 15.014 14119 Z= 0.289 Chirality : 0.036 0.187 1778 Planarity : 0.004 0.050 1722 Dihedral : 5.099 55.772 1448 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.58 % Allowed : 21.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.21), residues: 1288 helix: 3.64 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.43 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.001 0.000 HIS G 53 PHE 0.006 0.001 PHE E 18 TYR 0.005 0.001 TYR D 175 ARG 0.016 0.001 ARG B 21 *********************** 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 313 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 275 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8669 (t0) cc_final: 0.7870 (t0) REVERT: A 112 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8180 (t0) REVERT: A 138 MET cc_start: 0.9215 (tpp) cc_final: 0.8887 (mmm) REVERT: B 54 ASP cc_start: 0.8585 (t0) cc_final: 0.7690 (t70) REVERT: B 57 GLN cc_start: 0.8597 (mp10) cc_final: 0.8175 (mp10) REVERT: B 210 ASP cc_start: 0.8578 (m-30) cc_final: 0.8332 (m-30) REVERT: C 54 ASP cc_start: 0.8659 (t0) cc_final: 0.7720 (t0) REVERT: C 57 GLN cc_start: 0.8160 (mp10) cc_final: 0.7780 (mp10) REVERT: C 211 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: D 37 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8751 (mmmt) REVERT: D 57 GLN cc_start: 0.8523 (mp10) cc_final: 0.8233 (mp10) REVERT: D 142 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8325 (mp) REVERT: D 188 LYS cc_start: 0.8685 (tttt) cc_final: 0.8277 (ttmm) REVERT: E 54 ASP cc_start: 0.8658 (t0) cc_final: 0.8029 (t0) REVERT: E 57 GLN cc_start: 0.8672 (mp10) cc_final: 0.8326 (mp10) REVERT: F 54 ASP cc_start: 0.8575 (t0) cc_final: 0.8024 (t70) REVERT: F 62 MET cc_start: 0.7595 (mtp) cc_final: 0.7307 (mtp) REVERT: G 54 ASP cc_start: 0.8527 (t0) cc_final: 0.7829 (t0) REVERT: G 57 GLN cc_start: 0.8554 (mp10) cc_final: 0.8183 (mp10) REVERT: G 62 MET cc_start: 0.7350 (mtp) cc_final: 0.7076 (ttm) outliers start: 38 outliers final: 30 residues processed: 308 average time/residue: 0.2322 time to fit residues: 100.1399 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 : 1.370 ------------------------------------------------------------------------------- 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 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 9 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 C residue 211 GLU 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 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 112 ASN 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 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 143 LEU Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 0.0970 chunk 109 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 B 112 ASN B 238 ASN C 178 GLN D 178 GLN E 112 ASN E 226 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093104 restraints weight = 18526.882| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.74 r_work: 0.3028 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10423 Z= 0.190 Angle : 0.563 16.330 14119 Z= 0.294 Chirality : 0.036 0.178 1778 Planarity : 0.004 0.050 1722 Dihedral : 4.920 55.947 1445 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.70 (0.21), residues: 1288 helix: 3.63 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.43 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 139 HIS 0.002 0.000 HIS G 53 PHE 0.006 0.001 PHE E 18 TYR 0.006 0.001 TYR C 175 ARG 0.015 0.001 ARG B 21 ********************** 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 314 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8587 (t0) cc_final: 0.7650 (t0) REVERT: A 57 GLN cc_start: 0.8346 (mp10) cc_final: 0.7937 (mp10) REVERT: A 112 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8158 (t0) REVERT: A 138 MET cc_start: 0.9273 (tpp) cc_final: 0.8880 (mmm) REVERT: B 54 ASP cc_start: 0.8577 (t0) cc_final: 0.7707 (t0) REVERT: B 57 GLN cc_start: 0.8561 (mp10) cc_final: 0.8213 (mp10) REVERT: B 210 ASP cc_start: 0.8564 (m-30) cc_final: 0.8334 (m-30) REVERT: C 54 ASP cc_start: 0.8615 (t0) cc_final: 0.7643 (t0) REVERT: C 55 LEU cc_start: 0.7872 (mm) cc_final: 0.7574 (mm) REVERT: C 57 GLN cc_start: 0.8142 (mp10) cc_final: 0.7752 (mp10) REVERT: C 138 MET cc_start: 0.9439 (mmm) cc_final: 0.8254 (tpt) REVERT: C 211 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: D 37 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8754 (mmmt) REVERT: D 54 ASP cc_start: 0.8452 (t0) cc_final: 0.7934 (t0) REVERT: D 57 GLN cc_start: 0.8511 (mp10) cc_final: 0.8230 (mp10) REVERT: D 142 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8413 (mp) REVERT: D 188 LYS cc_start: 0.8682 (tttt) cc_final: 0.8268 (ttmm) REVERT: E 54 ASP cc_start: 0.8669 (t0) cc_final: 0.8084 (t0) REVERT: E 57 GLN cc_start: 0.8657 (mp10) cc_final: 0.8319 (mp10) REVERT: F 54 ASP cc_start: 0.8496 (t0) cc_final: 0.7980 (t0) REVERT: F 62 MET cc_start: 0.7587 (mtp) cc_final: 0.7303 (mtp) REVERT: G 54 ASP cc_start: 0.8441 (t0) cc_final: 0.7789 (t0) REVERT: G 57 GLN cc_start: 0.8496 (mp10) cc_final: 0.8165 (mp10) REVERT: G 62 MET cc_start: 0.7352 (mtp) cc_final: 0.7047 (ttm) outliers start: 32 outliers final: 24 residues processed: 312 average time/residue: 0.2220 time to fit residues: 96.6701 Evaluate side-chains 304 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 276 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 112 ASN 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 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 211 GLU 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 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 189 LEU Chi-restraints excluded: chain E residue 239 ILE 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 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 1.9990 chunk 124 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 B 112 ASN B 238 ASN C 178 GLN E 112 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092615 restraints weight = 18330.249| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.70 r_work: 0.3013 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10423 Z= 0.197 Angle : 0.556 13.320 14119 Z= 0.292 Chirality : 0.036 0.172 1778 Planarity : 0.004 0.048 1722 Dihedral : 4.821 55.682 1442 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.83 % Allowed : 22.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.61 (0.21), residues: 1288 helix: 3.58 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 139 HIS 0.001 0.000 HIS G 53 PHE 0.006 0.001 PHE E 18 TYR 0.004 0.001 TYR F 228 ARG 0.015 0.001 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4303.54 seconds wall clock time: 77 minutes 14.21 seconds (4634.21 seconds total)