Starting phenix.real_space_refine on Mon Jun 9 01:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqd_34024/06_2025/7yqd_34024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqd_34024/06_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_34024/06_2025/7yqd_34024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqd_34024/06_2025/7yqd_34024.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqd_34024/06_2025/7yqd_34024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqd_34024/06_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-5710/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: 3.68, 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: 2.56 Conformation dependent library (CDL) restraints added in 1.2 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: 0.88 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: 2.99 Time building geometry restraints manager: 3.00 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.430 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.038 10423 Z= 0.906 Angle : 1.460 5.669 14119 Z= 1.214 Chirality : 0.104 0.335 1778 Planarity : 0.005 0.022 1722 Dihedral : 13.548 58.363 3822 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 7.63 % Allowed : 7.92 % Favored : 84.45 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.24418 ( 931) hydrogen bonds : angle 5.36735 ( 2772) covalent geometry : bond 0.01154 (10423) covalent geometry : angle 1.45973 (14119) *********************** 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 : 1.277 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: 0.2682 time to fit residues: 154.4754 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 : 1.195 ------------------------------------------------------------------------------- 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 = 0.109897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.089062 restraints weight = 18394.064| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.64 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: 0.3369 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= 0.182 Angle : 0.540 8.803 14119 Z= 0.297 Chirality : 0.036 0.133 1778 Planarity : 0.004 0.043 1722 Dihedral : 8.186 58.974 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 Details of bonding type rmsd hydrogen bonds : bond 0.08573 ( 931) hydrogen bonds : angle 3.84221 ( 2772) covalent geometry : bond 0.00319 (10423) covalent geometry : angle 0.53959 (14119) *********************** 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 : 1.154 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: 0.8426 (mp10) cc_final: 0.8069 (mp10) REVERT: B 37 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9090 (mmtt) REVERT: B 54 ASP cc_start: 0.8680 (t0) cc_final: 0.8003 (t70) REVERT: B 62 MET cc_start: 0.7060 (mtp) cc_final: 0.6679 (ttm) REVERT: B 128 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8318 (mm) REVERT: B 166 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8442 (ttp-170) REVERT: C 54 ASP cc_start: 0.8553 (t0) cc_final: 0.7961 (t0) REVERT: C 166 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8535 (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: 0.8949 (mmtt) REVERT: D 54 ASP cc_start: 0.8719 (t0) cc_final: 0.8288 (t0) REVERT: D 166 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8602 (mtt90) REVERT: E 54 ASP cc_start: 0.8662 (t0) cc_final: 0.8015 (t0) REVERT: E 57 GLN cc_start: 0.8496 (mp10) cc_final: 0.8216 (mp10) REVERT: F 54 ASP cc_start: 0.8642 (t0) cc_final: 0.8156 (t0) REVERT: F 57 GLN cc_start: 0.8551 (mp10) cc_final: 0.8255 (mp10) REVERT: F 166 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8597 (ttp-170) REVERT: F 203 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7256 (mtp85) REVERT: F 210 ASP cc_start: 0.8368 (m-30) cc_final: 0.7979 (m-30) REVERT: G 54 ASP cc_start: 0.8652 (t0) cc_final: 0.7982 (t0) outliers start: 62 outliers final: 32 residues processed: 368 average time/residue: 0.2412 time to fit residues: 121.4513 Evaluate side-chains 340 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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: 4.9990 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 178 GLN A 238 ASN B 63 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.110031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.088644 restraints weight = 18679.043| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.68 r_work: 0.2954 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10423 Z= 0.160 Angle : 0.487 6.613 14119 Z= 0.267 Chirality : 0.035 0.125 1778 Planarity : 0.004 0.030 1722 Dihedral : 6.113 57.064 1464 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.45 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: 5.11 (0.20), residues: 1288 helix: 3.92 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.38 (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 Details of bonding type rmsd hydrogen bonds : bond 0.07496 ( 931) hydrogen bonds : angle 3.62346 ( 2772) covalent geometry : bond 0.00299 (10423) covalent geometry : angle 0.48678 (14119) *********************** 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 368 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8745 (t0) cc_final: 0.8149 (t70) REVERT: B 37 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9085 (mmtt) REVERT: B 54 ASP cc_start: 0.8628 (t0) cc_final: 0.7952 (t70) REVERT: B 166 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8535 (ttp-170) REVERT: B 210 ASP cc_start: 0.8671 (m-30) cc_final: 0.8362 (m-30) REVERT: C 54 ASP cc_start: 0.8598 (t0) cc_final: 0.8050 (t0) REVERT: C 142 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 166 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8691 (ttp-170) REVERT: D 37 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8807 (mmmt) REVERT: D 54 ASP cc_start: 0.8695 (t0) cc_final: 0.8168 (t0) REVERT: D 166 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8711 (mtt90) REVERT: D 188 LYS cc_start: 0.8832 (tttt) cc_final: 0.8481 (ttmm) REVERT: D 208 GLU cc_start: 0.8803 (tp30) cc_final: 0.8497 (tp30) REVERT: E 54 ASP cc_start: 0.8637 (t0) cc_final: 0.7972 (t0) REVERT: E 57 GLN cc_start: 0.8537 (mp10) cc_final: 0.8149 (mp10) REVERT: E 138 MET cc_start: 0.8411 (tpp) cc_final: 0.8208 (tpp) REVERT: E 158 GLN cc_start: 0.8546 (tt0) cc_final: 0.8294 (tt0) REVERT: F 54 ASP cc_start: 0.8639 (t0) cc_final: 0.8269 (t0) REVERT: F 203 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7288 (mtp85) REVERT: F 210 ASP cc_start: 0.8230 (m-30) cc_final: 0.7885 (m-30) REVERT: G 54 ASP cc_start: 0.8568 (t0) cc_final: 0.7753 (t0) REVERT: G 57 GLN cc_start: 0.8502 (mp10) cc_final: 0.8063 (mp10) outliers start: 55 outliers final: 38 residues processed: 346 average time/residue: 0.2557 time to fit residues: 121.6945 Evaluate side-chains 337 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 293 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 52 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: 0.0170 chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 0.0570 chunk 83 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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 114 GLN B 178 GLN B 238 ASN C 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 = 0.3440 r_free = 0.3440 target = 0.111639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090035 restraints weight = 18409.883| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.68 r_work: 0.2978 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10423 Z= 0.151 Angle : 0.476 6.063 14119 Z= 0.261 Chirality : 0.035 0.142 1778 Planarity : 0.003 0.028 1722 Dihedral : 6.069 56.900 1464 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.81 % Allowed : 19.42 % 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: 4.96 (0.20), residues: 1288 helix: 3.80 (0.13), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.30), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 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 0.008 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.06868 ( 931) hydrogen bonds : angle 3.51526 ( 2772) covalent geometry : bond 0.00284 (10423) covalent geometry : angle 0.47640 (14119) *********************** 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 353 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 302 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8716 (t0) cc_final: 0.8060 (t0) REVERT: A 210 ASP cc_start: 0.8425 (m-30) cc_final: 0.8215 (m-30) REVERT: B 37 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8896 (mmmt) REVERT: B 54 ASP cc_start: 0.8554 (t0) cc_final: 0.7874 (t70) REVERT: B 57 GLN cc_start: 0.8618 (mp10) cc_final: 0.8356 (mp10) REVERT: B 166 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8515 (ttp-170) REVERT: B 210 ASP cc_start: 0.8640 (m-30) cc_final: 0.8310 (m-30) REVERT: C 54 ASP cc_start: 0.8662 (t0) cc_final: 0.8149 (t0) REVERT: D 37 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8740 (mmmt) REVERT: D 54 ASP cc_start: 0.8673 (t0) cc_final: 0.8068 (t0) REVERT: D 57 GLN cc_start: 0.8526 (mp10) cc_final: 0.8174 (mp10) REVERT: D 188 LYS cc_start: 0.8769 (tttt) cc_final: 0.8366 (ttmm) REVERT: D 208 GLU cc_start: 0.8824 (tp30) cc_final: 0.8490 (tp30) REVERT: E 54 ASP cc_start: 0.8638 (t0) cc_final: 0.8109 (t0) REVERT: F 54 ASP cc_start: 0.8629 (t0) cc_final: 0.8105 (t0) REVERT: F 57 GLN cc_start: 0.8593 (mp10) cc_final: 0.8392 (mp10) REVERT: F 109 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6143 (mp) REVERT: F 166 ARG cc_start: 0.8614 (ttp-170) cc_final: 0.8238 (mtt90) REVERT: F 210 ASP cc_start: 0.8173 (m-30) cc_final: 0.7948 (m-30) REVERT: G 54 ASP cc_start: 0.8596 (t0) cc_final: 0.7768 (t0) REVERT: G 57 GLN cc_start: 0.8561 (mp10) cc_final: 0.8309 (mp10) outliers start: 51 outliers final: 34 residues processed: 336 average time/residue: 0.2750 time to fit residues: 129.7641 Evaluate side-chains 327 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 239 ILE Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN C 112 ASN C 178 GLN D 178 GLN E 238 ASN G 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.090966 restraints weight = 18447.916| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.72 r_work: 0.2991 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10423 Z= 0.147 Angle : 0.486 7.107 14119 Z= 0.263 Chirality : 0.035 0.127 1778 Planarity : 0.004 0.033 1722 Dihedral : 5.902 56.762 1462 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.68 % Allowed : 19.70 % Favored : 76.63 % 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: 4.89 (0.21), residues: 1288 helix: 3.74 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.23 (0.32), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 A 183 ARG 0.011 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.06482 ( 931) hydrogen bonds : angle 3.46500 ( 2772) covalent geometry : bond 0.00279 (10423) covalent geometry : angle 0.48590 (14119) *********************** 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 339 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8729 (t0) cc_final: 0.8123 (t0) REVERT: B 37 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8845 (mmmt) REVERT: B 54 ASP cc_start: 0.8579 (t0) cc_final: 0.7770 (t70) REVERT: B 57 GLN cc_start: 0.8653 (mp10) cc_final: 0.8374 (mp10) REVERT: B 210 ASP cc_start: 0.8493 (m-30) cc_final: 0.8212 (m-30) REVERT: C 54 ASP cc_start: 0.8599 (t0) cc_final: 0.7895 (t0) REVERT: C 142 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (mp) REVERT: C 211 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8177 (tp30) REVERT: D 37 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8739 (mmmt) REVERT: D 54 ASP cc_start: 0.8725 (t0) cc_final: 0.8046 (t0) REVERT: D 57 GLN cc_start: 0.8556 (mp10) cc_final: 0.8168 (mp10) REVERT: D 142 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8464 (mp) REVERT: D 188 LYS cc_start: 0.8775 (tttt) cc_final: 0.8368 (ttmm) REVERT: D 208 GLU cc_start: 0.8821 (tp30) cc_final: 0.8469 (tp30) REVERT: E 54 ASP cc_start: 0.8606 (t0) cc_final: 0.7943 (t0) REVERT: E 57 GLN cc_start: 0.8562 (mp10) cc_final: 0.8185 (mp10) REVERT: E 227 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8306 (mm-40) REVERT: F 54 ASP cc_start: 0.8636 (t0) cc_final: 0.8066 (t70) REVERT: F 57 GLN cc_start: 0.8595 (mp10) cc_final: 0.8382 (mp10) REVERT: F 109 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.6090 (mp) REVERT: F 166 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8304 (mtt90) REVERT: G 54 ASP cc_start: 0.8635 (t0) cc_final: 0.7742 (t0) REVERT: G 57 GLN cc_start: 0.8581 (mp10) cc_final: 0.8308 (mp10) outliers start: 39 outliers final: 30 residues processed: 328 average time/residue: 0.2360 time to fit residues: 107.8543 Evaluate side-chains 317 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 37 LYS 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 239 ILE 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 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 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 239 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 239 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 238 ASN B 178 GLN B 226 ASN B 238 ASN C 112 ASN C 178 GLN C 226 ASN D 226 ASN E 238 ASN F 178 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090773 restraints weight = 18497.139| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.71 r_work: 0.2990 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10423 Z= 0.149 Angle : 0.493 6.313 14119 Z= 0.267 Chirality : 0.035 0.126 1778 Planarity : 0.003 0.033 1722 Dihedral : 5.788 56.316 1460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 4.15 % Allowed : 20.26 % 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: 4.84 (0.21), residues: 1288 helix: 3.70 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.21 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 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 0.011 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.06359 ( 931) hydrogen bonds : angle 3.47013 ( 2772) covalent geometry : bond 0.00294 (10423) covalent geometry : angle 0.49316 (14119) *********************** 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 331 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8829 (t0) cc_final: 0.7644 (t0) REVERT: A 57 GLN cc_start: 0.8428 (mp10) cc_final: 0.7769 (mp10) REVERT: A 210 ASP cc_start: 0.8382 (m-30) cc_final: 0.8152 (m-30) REVERT: B 37 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8838 (mmmt) REVERT: B 54 ASP cc_start: 0.8628 (t0) cc_final: 0.7796 (t70) REVERT: B 57 GLN cc_start: 0.8668 (mp10) cc_final: 0.8360 (mp10) REVERT: B 210 ASP cc_start: 0.8560 (m-30) cc_final: 0.8250 (m-30) REVERT: C 54 ASP cc_start: 0.8641 (t0) cc_final: 0.7996 (t0) REVERT: C 142 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 210 ASP cc_start: 0.8415 (m-30) cc_final: 0.8186 (m-30) REVERT: D 37 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8716 (mmmt) REVERT: D 54 ASP cc_start: 0.8663 (t0) cc_final: 0.8089 (t0) REVERT: D 142 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8426 (mp) REVERT: D 188 LYS cc_start: 0.8743 (tttt) cc_final: 0.8329 (ttmm) REVERT: D 208 GLU cc_start: 0.8839 (tp30) cc_final: 0.8481 (tp30) REVERT: E 54 ASP cc_start: 0.8629 (t0) cc_final: 0.7567 (t0) REVERT: E 57 GLN cc_start: 0.8609 (mp10) cc_final: 0.8064 (mp10) REVERT: F 54 ASP cc_start: 0.8694 (t0) cc_final: 0.8080 (t70) REVERT: F 57 GLN cc_start: 0.8547 (mp10) cc_final: 0.8330 (mp10) REVERT: F 62 MET cc_start: 0.7525 (mtp) cc_final: 0.7253 (mtp) REVERT: F 166 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.8298 (mtt90) REVERT: G 54 ASP cc_start: 0.8649 (t0) cc_final: 0.8007 (t0) REVERT: G 62 MET cc_start: 0.7317 (mtp) cc_final: 0.7066 (ttm) REVERT: G 138 MET cc_start: 0.9390 (mmm) cc_final: 0.9125 (tpt) REVERT: G 166 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8471 (mtm-85) outliers start: 44 outliers final: 34 residues processed: 323 average time/residue: 0.2521 time to fit residues: 113.5619 Evaluate side-chains 318 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 37 LYS 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 B residue 239 ILE 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 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 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 142 LEU Chi-restraints excluded: chain G residue 143 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 166 ARG 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: 0.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 112 ASN B 178 GLN B 238 ASN C 112 ASN C 178 GLN D 178 GLN F 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093682 restraints weight = 18599.919| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.73 r_work: 0.3035 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4960 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= 0.139 Angle : 0.488 5.977 14119 Z= 0.264 Chirality : 0.035 0.124 1778 Planarity : 0.004 0.046 1722 Dihedral : 5.619 56.561 1458 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.96 % Allowed : 20.26 % 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: 3.70 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.17 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 139 HIS 0.001 0.000 HIS F 59 PHE 0.005 0.001 PHE C 18 TYR 0.005 0.001 TYR B 214 ARG 0.014 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05841 ( 931) hydrogen bonds : angle 3.40025 ( 2772) covalent geometry : bond 0.00257 (10423) covalent geometry : angle 0.48794 (14119) *********************** 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 332 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8757 (t0) cc_final: 0.7741 (t0) REVERT: A 57 GLN cc_start: 0.8408 (mp10) cc_final: 0.7907 (mp10) REVERT: B 37 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8796 (mmmt) REVERT: B 54 ASP cc_start: 0.8549 (t0) cc_final: 0.7766 (t70) REVERT: B 57 GLN cc_start: 0.8668 (mp10) cc_final: 0.8424 (mp10) REVERT: B 210 ASP cc_start: 0.8525 (m-30) cc_final: 0.8260 (m-30) REVERT: C 54 ASP cc_start: 0.8601 (t0) cc_final: 0.7754 (t0) REVERT: C 57 GLN cc_start: 0.8148 (mp10) cc_final: 0.7842 (mp10) REVERT: C 210 ASP cc_start: 0.8322 (m-30) cc_final: 0.8121 (m-30) REVERT: D 37 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8660 (mmmt) REVERT: D 54 ASP cc_start: 0.8621 (t0) cc_final: 0.8085 (t0) REVERT: D 57 GLN cc_start: 0.8519 (mp10) cc_final: 0.8248 (mp10) REVERT: D 188 LYS cc_start: 0.8684 (tttt) cc_final: 0.8288 (ttmm) REVERT: E 54 ASP cc_start: 0.8611 (t0) cc_final: 0.7514 (t0) REVERT: E 57 GLN cc_start: 0.8636 (mp10) cc_final: 0.8102 (mp10) REVERT: F 54 ASP cc_start: 0.8656 (t0) cc_final: 0.8055 (t70) REVERT: F 57 GLN cc_start: 0.8547 (mp10) cc_final: 0.8343 (mp10) REVERT: F 62 MET cc_start: 0.7449 (mtp) cc_final: 0.7231 (mtp) REVERT: F 210 ASP cc_start: 0.8198 (m-30) cc_final: 0.7871 (m-30) REVERT: G 54 ASP cc_start: 0.8617 (t0) cc_final: 0.7911 (t0) REVERT: G 57 GLN cc_start: 0.8623 (mp10) cc_final: 0.8418 (mp10) REVERT: G 62 MET cc_start: 0.7286 (mtp) cc_final: 0.7058 (ttm) outliers start: 42 outliers final: 29 residues processed: 323 average time/residue: 0.2196 time to fit residues: 100.5293 Evaluate side-chains 302 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 271 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 9 GLN Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 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 178 GLN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 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 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 142 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: 0.5980 chunk 119 optimal weight: 0.0040 chunk 77 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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 112 ASN B 178 GLN B 238 ASN D 178 GLN E 226 ASN E 238 ASN ** G 112 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 = 0.3508 r_free = 0.3508 target = 0.116596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094597 restraints weight = 18508.499| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.74 r_work: 0.3051 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10423 Z= 0.140 Angle : 0.526 13.794 14119 Z= 0.276 Chirality : 0.035 0.131 1778 Planarity : 0.004 0.046 1722 Dihedral : 5.429 56.656 1454 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.68 % Allowed : 20.83 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.79 (0.21), residues: 1288 helix: 3.66 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.19 (0.33), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 F 228 ARG 0.015 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 931) hydrogen bonds : angle 3.39622 ( 2772) covalent geometry : bond 0.00266 (10423) covalent geometry : angle 0.52589 (14119) *********************** 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 320 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8719 (t0) cc_final: 0.7698 (t0) REVERT: A 57 GLN cc_start: 0.8389 (mp10) cc_final: 0.7853 (mp10) REVERT: B 37 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8784 (mmmt) REVERT: B 54 ASP cc_start: 0.8516 (t0) cc_final: 0.7683 (t70) REVERT: B 57 GLN cc_start: 0.8662 (mp10) cc_final: 0.8267 (mp10) REVERT: B 208 GLU cc_start: 0.8616 (tp30) cc_final: 0.8414 (tp30) REVERT: B 210 ASP cc_start: 0.8508 (m-30) cc_final: 0.8301 (m-30) REVERT: C 54 ASP cc_start: 0.8581 (t0) cc_final: 0.7692 (t0) REVERT: C 57 GLN cc_start: 0.8150 (mp10) cc_final: 0.7885 (mp10) REVERT: D 37 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8761 (mmmt) REVERT: D 57 GLN cc_start: 0.8537 (mp10) cc_final: 0.8317 (mp10) REVERT: E 54 ASP cc_start: 0.8611 (t0) cc_final: 0.7531 (t0) REVERT: E 57 GLN cc_start: 0.8625 (mp10) cc_final: 0.8121 (mp10) REVERT: E 227 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8235 (mm-40) REVERT: F 54 ASP cc_start: 0.8660 (t0) cc_final: 0.8048 (t70) REVERT: F 62 MET cc_start: 0.7500 (mtp) cc_final: 0.7210 (mtp) REVERT: F 210 ASP cc_start: 0.8206 (m-30) cc_final: 0.7905 (m-30) REVERT: G 54 ASP cc_start: 0.8621 (t0) cc_final: 0.7811 (t0) REVERT: G 57 GLN cc_start: 0.8659 (mp10) cc_final: 0.8300 (mp10) REVERT: G 62 MET cc_start: 0.7271 (mtp) cc_final: 0.7034 (ttm) outliers start: 39 outliers final: 29 residues processed: 312 average time/residue: 0.2293 time to fit residues: 103.6150 Evaluate side-chains 309 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 37 LYS 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 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 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 55 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain 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 138 MET Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 177 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 5.9990 chunk 6 optimal weight: 0.0170 chunk 106 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 D 178 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.115909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093891 restraints weight = 18485.297| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.75 r_work: 0.3042 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5196 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= 0.143 Angle : 0.539 14.587 14119 Z= 0.282 Chirality : 0.036 0.189 1778 Planarity : 0.004 0.047 1722 Dihedral : 5.358 56.477 1451 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.83 % Allowed : 21.30 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.62 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.27 (0.34), 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 0.006 0.001 PHE C 33 TYR 0.004 0.001 TYR E 183 ARG 0.016 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05711 ( 931) hydrogen bonds : angle 3.43594 ( 2772) covalent geometry : bond 0.00282 (10423) covalent geometry : angle 0.53909 (14119) *********************** 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 311 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 281 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8653 (t0) cc_final: 0.7578 (t0) REVERT: A 57 GLN cc_start: 0.8394 (mp10) cc_final: 0.7809 (mp10) REVERT: B 37 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8766 (mmmt) REVERT: B 54 ASP cc_start: 0.8521 (t0) cc_final: 0.7757 (t0) REVERT: B 57 GLN cc_start: 0.8665 (mp10) cc_final: 0.8297 (mp10) REVERT: B 208 GLU cc_start: 0.8665 (tp30) cc_final: 0.8458 (tp30) REVERT: B 210 ASP cc_start: 0.8547 (m-30) cc_final: 0.8277 (m-30) REVERT: C 54 ASP cc_start: 0.8655 (t0) cc_final: 0.7708 (t0) REVERT: C 57 GLN cc_start: 0.8240 (mp10) cc_final: 0.7870 (mp10) REVERT: D 37 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8739 (mmmt) REVERT: D 54 ASP cc_start: 0.8521 (t0) cc_final: 0.8016 (t0) REVERT: D 57 GLN cc_start: 0.8531 (mp10) cc_final: 0.8253 (mp10) REVERT: E 54 ASP cc_start: 0.8639 (t0) cc_final: 0.7526 (t0) REVERT: E 57 GLN cc_start: 0.8606 (mp10) cc_final: 0.8061 (mp10) REVERT: E 227 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8230 (mm-40) REVERT: F 54 ASP cc_start: 0.8642 (t0) cc_final: 0.8285 (t70) REVERT: F 62 MET cc_start: 0.7547 (mtp) cc_final: 0.7278 (mtp) REVERT: F 210 ASP cc_start: 0.8223 (m-30) cc_final: 0.7911 (m-30) REVERT: G 54 ASP cc_start: 0.8637 (t0) cc_final: 0.7783 (t0) REVERT: G 57 GLN cc_start: 0.8667 (mp10) cc_final: 0.8287 (mp10) REVERT: G 62 MET cc_start: 0.7342 (mtp) cc_final: 0.7085 (ttm) outliers start: 30 outliers final: 26 residues processed: 306 average time/residue: 0.2287 time to fit residues: 99.8458 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 : 1.374 ------------------------------------------------------------------------------- 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 37 LYS Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE 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 178 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 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 142 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 178 GLN D 178 GLN E 226 ASN E 238 ASN F 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.092788 restraints weight = 18414.523| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.73 r_work: 0.3021 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5183 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= 0.149 Angle : 0.540 12.011 14119 Z= 0.286 Chirality : 0.036 0.180 1778 Planarity : 0.004 0.048 1722 Dihedral : 5.262 56.029 1450 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 3.02 % Allowed : 21.58 % 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: 4.61 (0.21), residues: 1288 helix: 3.56 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 139 HIS 0.001 0.000 HIS D 59 PHE 0.006 0.001 PHE D 33 TYR 0.009 0.001 TYR A 175 ARG 0.015 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 931) hydrogen bonds : angle 3.47504 ( 2772) covalent geometry : bond 0.00302 (10423) covalent geometry : angle 0.53988 (14119) ********************** 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 307 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8593 (t0) cc_final: 0.7479 (t0) REVERT: A 57 GLN cc_start: 0.8397 (mp10) cc_final: 0.7774 (mp10) REVERT: A 112 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 138 MET cc_start: 0.9030 (tpp) cc_final: 0.8548 (tpp) REVERT: B 37 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8763 (mmmt) REVERT: B 54 ASP cc_start: 0.8525 (t0) cc_final: 0.7804 (t0) REVERT: B 57 GLN cc_start: 0.8684 (mp10) cc_final: 0.8356 (mp10) REVERT: B 189 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8646 (mm) REVERT: B 208 GLU cc_start: 0.8684 (tp30) cc_final: 0.8478 (tp30) REVERT: B 210 ASP cc_start: 0.8571 (m-30) cc_final: 0.8320 (m-30) REVERT: C 54 ASP cc_start: 0.8693 (t0) cc_final: 0.7743 (t0) REVERT: C 57 GLN cc_start: 0.8248 (mp10) cc_final: 0.7860 (mp10) REVERT: D 37 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8749 (mmmt) REVERT: D 54 ASP cc_start: 0.8499 (t0) cc_final: 0.7939 (t0) REVERT: D 57 GLN cc_start: 0.8536 (mp10) cc_final: 0.8240 (mp10) REVERT: E 54 ASP cc_start: 0.8660 (t0) cc_final: 0.8116 (t0) REVERT: E 57 GLN cc_start: 0.8613 (mp10) cc_final: 0.8367 (mp10) REVERT: F 54 ASP cc_start: 0.8675 (t0) cc_final: 0.8075 (t70) REVERT: F 62 MET cc_start: 0.7553 (mtp) cc_final: 0.7288 (mtp) REVERT: F 138 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9118 (mmm) REVERT: F 210 ASP cc_start: 0.8246 (m-30) cc_final: 0.7989 (m-30) REVERT: G 54 ASP cc_start: 0.8640 (t0) cc_final: 0.7788 (t0) REVERT: G 57 GLN cc_start: 0.8695 (mp10) cc_final: 0.8298 (mp10) REVERT: G 62 MET cc_start: 0.7381 (mtp) cc_final: 0.7104 (ttm) outliers start: 32 outliers final: 24 residues processed: 304 average time/residue: 0.2443 time to fit residues: 104.6719 Evaluate side-chains 295 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 GLN Chi-restraints excluded: chain B residue 37 LYS 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 178 GLN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 239 ILE 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 189 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain F residue 138 MET 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 155 VAL Chi-restraints excluded: chain G residue 177 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 51 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN B 178 GLN D 178 GLN E 226 ASN F 178 GLN G 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.093083 restraints weight = 18218.279| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.73 r_work: 0.3028 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10423 Z= 0.144 Angle : 0.533 11.623 14119 Z= 0.282 Chirality : 0.036 0.191 1778 Planarity : 0.004 0.046 1722 Dihedral : 5.195 55.974 1449 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.73 % Allowed : 21.96 % 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: 4.63 (0.21), residues: 1288 helix: 3.58 (0.14), residues: 1092 sheet: None (None), residues: 0 loop : -0.44 (0.34), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 139 HIS 0.001 0.000 HIS D 59 PHE 0.006 0.001 PHE E 18 TYR 0.004 0.001 TYR F 228 ARG 0.014 0.001 ARG B 21 Details of bonding type rmsd hydrogen bonds : bond 0.05822 ( 931) hydrogen bonds : angle 3.45875 ( 2772) covalent geometry : bond 0.00282 (10423) covalent geometry : angle 0.53331 (14119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5143.87 seconds wall clock time: 93 minutes 10.71 seconds (5590.71 seconds total)