Starting phenix.real_space_refine on Wed Mar 4 02:43:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cky_16706/03_2026/8cky_16706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cky_16706/03_2026/8cky_16706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cky_16706/03_2026/8cky_16706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cky_16706/03_2026/8cky_16706.map" model { file = "/net/cci-nas-00/data/ceres_data/8cky_16706/03_2026/8cky_16706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cky_16706/03_2026/8cky_16706.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 72 5.16 5 C 6546 2.51 5 N 1788 2.21 5 O 1932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1647 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 76 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 1.55, per 1000 atoms: 0.15 Number of scatterers: 10338 At special positions: 0 Unit cell: (110.67, 112.53, 72.54, 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 72 16.00 O 1932 8.00 N 1788 7.00 C 6546 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: 0.72 Conformation dependent library (CDL) restraints added in 503.6 milliseconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 70.1% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL I 59 " --> pdb=" O MET I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 119 Processing helix chain 'I' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS I 140 " --> pdb=" O LEU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.746A pdb=" N VAL K 59 " --> pdb=" O MET K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 119 Processing helix chain 'K' and resid 125 through 146 removed outlier: 3.729A pdb=" N LYS K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 176 Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.219A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 205 removed outlier: 3.679A pdb=" N LEU K 205 " --> pdb=" O ILE K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4 642 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3420 1.34 - 1.46: 1176 1.46 - 1.58: 5838 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10566 Sorted by residual: bond pdb=" CB PRO E 1 " pdb=" CG PRO E 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.06e+00 bond pdb=" CB PRO K 1 " pdb=" CG PRO K 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.06e+00 bond pdb=" CB PRO C 1 " pdb=" CG PRO C 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.05e+00 bond pdb=" CB PRO I 1 " pdb=" CG PRO I 1 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.05e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.04e+00 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 12034 1.03 - 2.06: 1944 2.06 - 3.08: 272 3.08 - 4.11: 90 4.11 - 5.14: 24 Bond angle restraints: 14364 Sorted by residual: angle pdb=" CA GLN I 176 " pdb=" CB GLN I 176 " pdb=" CG GLN I 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN C 176 " pdb=" CB GLN C 176 " pdb=" CG GLN C 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN K 176 " pdb=" CB GLN K 176 " pdb=" CG GLN K 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN E 176 " pdb=" CB GLN E 176 " pdb=" CG GLN E 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA GLN G 176 " pdb=" CB GLN G 176 " pdb=" CG GLN G 176 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 ... (remaining 14359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 5952 16.27 - 32.54: 336 32.54 - 48.81: 66 48.81 - 65.08: 36 65.08 - 81.35: 12 Dihedral angle restraints: 6402 sinusoidal: 2544 harmonic: 3858 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA PHE G 32 " pdb=" C PHE G 32 " pdb=" N SER G 33 " pdb=" CA SER G 33 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 6399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 988 0.037 - 0.073: 459 0.073 - 0.109: 133 0.109 - 0.146: 40 0.146 - 0.182: 12 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA GLN E 176 " pdb=" N GLN E 176 " pdb=" C GLN E 176 " pdb=" CB GLN E 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA GLN K 176 " pdb=" N GLN K 176 " pdb=" C GLN K 176 " pdb=" CB GLN K 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA GLN C 176 " pdb=" N GLN C 176 " pdb=" C GLN C 176 " pdb=" CB GLN C 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 1629 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 132 " 0.198 9.50e-02 1.11e+02 8.90e-02 4.87e+00 pdb=" NE ARG E 132 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 132 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 132 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 132 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 132 " -0.198 9.50e-02 1.11e+02 8.90e-02 4.87e+00 pdb=" NE ARG K 132 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG K 132 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG K 132 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 132 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 132 " 0.198 9.50e-02 1.11e+02 8.89e-02 4.87e+00 pdb=" NE ARG I 132 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG I 132 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 132 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG I 132 " 0.006 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 24 2.53 - 3.12: 8088 3.12 - 3.71: 16804 3.71 - 4.31: 24528 4.31 - 4.90: 39410 Nonbonded interactions: 88854 Sorted by model distance: nonbonded pdb=" CB ALA I 14 " pdb=" OE1 GLU K 45 " model vdw 1.934 3.460 nonbonded pdb=" CB ALA C 14 " pdb=" OE1 GLU E 45 " model vdw 1.934 3.460 nonbonded pdb=" CB ALA G 14 " pdb=" OE1 GLU I 45 " model vdw 1.935 3.460 nonbonded pdb=" CB ALA A 14 " pdb=" OE1 GLU C 45 " model vdw 1.935 3.460 nonbonded pdb=" OE1 GLU A 45 " pdb=" CB ALA K 14 " model vdw 1.935 3.460 ... (remaining 88849 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.004 0.072 10566 Z= 0.214 Angle : 0.819 5.138 14364 Z= 0.485 Chirality : 0.047 0.182 1632 Planarity : 0.009 0.089 1854 Dihedral : 12.580 81.351 3894 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.54 % Allowed : 0.00 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1308 helix: 0.04 (0.15), residues: 876 sheet: -2.54 (0.33), residues: 54 loop : 1.35 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG K 167 TYR 0.017 0.004 TYR E 169 PHE 0.013 0.003 PHE G 40 TRP 0.018 0.005 TRP G 184 HIS 0.009 0.003 HIS I 12 Details of bonding type rmsd covalent geometry : bond 0.00423 (10566) covalent geometry : angle 0.81888 (14364) hydrogen bonds : bond 0.11910 ( 642) hydrogen bonds : angle 5.65430 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 348 time to evaluate : 0.425 Fit side-chains REVERT: A 18 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6982 (ttt-90) REVERT: A 25 LYS cc_start: 0.7968 (mttt) cc_final: 0.7429 (mttp) REVERT: A 51 ASP cc_start: 0.8303 (m-30) cc_final: 0.7869 (m-30) REVERT: A 145 TYR cc_start: 0.8198 (m-80) cc_final: 0.7973 (m-10) REVERT: A 175 GLU cc_start: 0.7202 (tt0) cc_final: 0.6954 (mt-10) REVERT: A 187 GLU cc_start: 0.6583 (mt-10) cc_final: 0.6353 (pt0) REVERT: C 25 LYS cc_start: 0.8017 (mttt) cc_final: 0.7401 (mttp) REVERT: C 39 MET cc_start: 0.8325 (tpt) cc_final: 0.8107 (tpp) REVERT: C 51 ASP cc_start: 0.8363 (m-30) cc_final: 0.7958 (m-30) REVERT: C 66 MET cc_start: 0.8510 (mmm) cc_final: 0.8211 (mmm) REVERT: C 118 MET cc_start: 0.8752 (mtp) cc_final: 0.8410 (mtp) REVERT: C 175 GLU cc_start: 0.7197 (tt0) cc_final: 0.6928 (mt-10) REVERT: E 25 LYS cc_start: 0.8040 (mttt) cc_final: 0.7755 (ttmm) REVERT: E 103 ASP cc_start: 0.8244 (m-30) cc_final: 0.8012 (m-30) REVERT: E 144 MET cc_start: 0.8073 (ttm) cc_final: 0.7849 (ttp) REVERT: E 175 GLU cc_start: 0.7172 (tt0) cc_final: 0.6904 (mm-30) REVERT: E 187 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6375 (pt0) REVERT: G 18 ARG cc_start: 0.7334 (ttp-170) cc_final: 0.6961 (ttt-90) REVERT: G 25 LYS cc_start: 0.7965 (mttt) cc_final: 0.7427 (mttp) REVERT: G 51 ASP cc_start: 0.8304 (m-30) cc_final: 0.7871 (m-30) REVERT: G 145 TYR cc_start: 0.8201 (m-80) cc_final: 0.7975 (m-10) REVERT: G 175 GLU cc_start: 0.7208 (tt0) cc_final: 0.6956 (mt-10) REVERT: G 187 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6352 (pt0) REVERT: I 25 LYS cc_start: 0.8016 (mttt) cc_final: 0.7401 (mttp) REVERT: I 39 MET cc_start: 0.8326 (tpt) cc_final: 0.8109 (tpp) REVERT: I 51 ASP cc_start: 0.8364 (m-30) cc_final: 0.7957 (m-30) REVERT: I 66 MET cc_start: 0.8513 (mmm) cc_final: 0.8212 (mmm) REVERT: I 118 MET cc_start: 0.8752 (mtp) cc_final: 0.8410 (mtp) REVERT: I 175 GLU cc_start: 0.7195 (tt0) cc_final: 0.6925 (mt-10) REVERT: K 25 LYS cc_start: 0.8037 (mttt) cc_final: 0.7753 (ttmm) REVERT: K 103 ASP cc_start: 0.8242 (m-30) cc_final: 0.8012 (m-30) REVERT: K 144 MET cc_start: 0.8076 (ttm) cc_final: 0.7852 (ttp) REVERT: K 175 GLU cc_start: 0.7173 (tt0) cc_final: 0.6903 (mm-30) REVERT: K 187 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6374 (pt0) outliers start: 6 outliers final: 0 residues processed: 348 average time/residue: 0.6248 time to fit residues: 231.3384 Evaluate side-chains 290 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0060 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 112 GLN A 193 ASN C 21 ASN C 112 GLN C 192 GLN C 219 GLN E 21 ASN E 112 GLN E 192 GLN E 193 ASN E 219 GLN G 50 GLN G 112 GLN G 193 ASN I 21 ASN I 112 GLN I 192 GLN I 219 GLN K 21 ASN K 112 GLN K 192 GLN K 193 ASN K 219 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114356 restraints weight = 10478.951| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.30 r_work: 0.3250 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10566 Z= 0.164 Angle : 0.525 6.009 14364 Z= 0.268 Chirality : 0.042 0.131 1632 Planarity : 0.005 0.032 1854 Dihedral : 4.683 22.584 1410 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.44 % Allowed : 10.05 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.22), residues: 1308 helix: 1.63 (0.17), residues: 888 sheet: -1.19 (0.46), residues: 54 loop : 0.71 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 154 TYR 0.008 0.001 TYR G 169 PHE 0.011 0.002 PHE A 32 TRP 0.007 0.001 TRP A 117 HIS 0.003 0.001 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.00415 (10566) covalent geometry : angle 0.52532 (14364) hydrogen bonds : bond 0.03840 ( 642) hydrogen bonds : angle 3.70036 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 0.448 Fit side-chains REVERT: A 18 ARG cc_start: 0.7630 (ttp-170) cc_final: 0.7049 (ttt-90) REVERT: A 21 ASN cc_start: 0.8254 (t0) cc_final: 0.7917 (m110) REVERT: A 25 LYS cc_start: 0.7945 (mttt) cc_final: 0.7663 (ttmm) REVERT: A 30 LYS cc_start: 0.7552 (mttt) cc_final: 0.7279 (mmtp) REVERT: A 145 TYR cc_start: 0.8323 (m-80) cc_final: 0.8091 (m-10) REVERT: A 154 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7559 (mtp85) REVERT: A 175 GLU cc_start: 0.7917 (tt0) cc_final: 0.7574 (mm-30) REVERT: A 187 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6427 (pt0) REVERT: C 25 LYS cc_start: 0.8040 (mttt) cc_final: 0.7718 (ttmm) REVERT: C 51 ASP cc_start: 0.8831 (m-30) cc_final: 0.8375 (m-30) REVERT: C 66 MET cc_start: 0.8981 (mmm) cc_final: 0.8736 (mmt) REVERT: C 118 MET cc_start: 0.8746 (mtp) cc_final: 0.8444 (mtp) REVERT: C 175 GLU cc_start: 0.8027 (tt0) cc_final: 0.7624 (mt-10) REVERT: C 192 GLN cc_start: 0.7952 (tp40) cc_final: 0.7579 (tm-30) REVERT: C 212 GLU cc_start: 0.7283 (tt0) cc_final: 0.6876 (tt0) REVERT: E 25 LYS cc_start: 0.7958 (mttt) cc_final: 0.7624 (ttmm) REVERT: E 136 LEU cc_start: 0.8819 (mp) cc_final: 0.8593 (mt) REVERT: E 175 GLU cc_start: 0.8064 (tt0) cc_final: 0.7727 (mt-10) REVERT: E 187 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6337 (pt0) REVERT: E 192 GLN cc_start: 0.8022 (tp40) cc_final: 0.7725 (tm-30) REVERT: G 18 ARG cc_start: 0.7585 (ttp-170) cc_final: 0.6992 (ttt-90) REVERT: G 21 ASN cc_start: 0.8241 (t0) cc_final: 0.7908 (m110) REVERT: G 25 LYS cc_start: 0.7950 (mttt) cc_final: 0.7668 (ttmm) REVERT: G 30 LYS cc_start: 0.7536 (mttt) cc_final: 0.7264 (mmtp) REVERT: G 145 TYR cc_start: 0.8328 (m-80) cc_final: 0.8095 (m-10) REVERT: G 154 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7564 (mtp85) REVERT: G 175 GLU cc_start: 0.7890 (tt0) cc_final: 0.7553 (mm-30) REVERT: G 187 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6426 (pt0) REVERT: I 25 LYS cc_start: 0.8055 (mttt) cc_final: 0.7732 (ttmm) REVERT: I 51 ASP cc_start: 0.8818 (m-30) cc_final: 0.8354 (m-30) REVERT: I 66 MET cc_start: 0.8999 (mmm) cc_final: 0.8758 (mmt) REVERT: I 118 MET cc_start: 0.8739 (mtp) cc_final: 0.8434 (mtp) REVERT: I 175 GLU cc_start: 0.8028 (tt0) cc_final: 0.7626 (mt-10) REVERT: I 192 GLN cc_start: 0.7968 (tp40) cc_final: 0.7596 (tm-30) REVERT: I 212 GLU cc_start: 0.7291 (tt0) cc_final: 0.6889 (tt0) REVERT: K 25 LYS cc_start: 0.7959 (mttt) cc_final: 0.7626 (ttmm) REVERT: K 136 LEU cc_start: 0.8805 (mp) cc_final: 0.8575 (mt) REVERT: K 175 GLU cc_start: 0.8059 (tt0) cc_final: 0.7716 (mt-10) REVERT: K 187 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6308 (pt0) REVERT: K 192 GLN cc_start: 0.7992 (tp40) cc_final: 0.7693 (tm-30) outliers start: 49 outliers final: 15 residues processed: 312 average time/residue: 0.6686 time to fit residues: 221.0051 Evaluate side-chains 297 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 282 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 80 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 193 ASN A 219 GLN C 112 GLN C 179 GLN C 193 ASN C 219 GLN E 112 GLN E 179 GLN E 193 ASN G 50 GLN G 193 ASN G 219 GLN I 112 GLN I 179 GLN I 193 ASN I 219 GLN K 112 GLN K 179 GLN K 193 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115142 restraints weight = 10570.989| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.26 r_work: 0.3254 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10566 Z= 0.142 Angle : 0.503 6.765 14364 Z= 0.250 Chirality : 0.042 0.154 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.303 20.019 1410 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.62 % Allowed : 13.32 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.22), residues: 1308 helix: 1.82 (0.17), residues: 894 sheet: -0.55 (0.56), residues: 54 loop : 0.53 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 154 TYR 0.008 0.001 TYR E 145 PHE 0.011 0.002 PHE E 32 TRP 0.005 0.001 TRP G 117 HIS 0.002 0.000 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00353 (10566) covalent geometry : angle 0.50271 (14364) hydrogen bonds : bond 0.03510 ( 642) hydrogen bonds : angle 3.42349 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.392 Fit side-chains REVERT: A 18 ARG cc_start: 0.7384 (ttp-170) cc_final: 0.6738 (ttt-90) REVERT: A 21 ASN cc_start: 0.8149 (t0) cc_final: 0.7790 (m110) REVERT: A 25 LYS cc_start: 0.8000 (mttt) cc_final: 0.7684 (ttmm) REVERT: A 145 TYR cc_start: 0.8299 (m-80) cc_final: 0.8053 (m-10) REVERT: A 148 THR cc_start: 0.7826 (m) cc_final: 0.7533 (t) REVERT: A 154 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7528 (mtp85) REVERT: A 175 GLU cc_start: 0.7873 (tt0) cc_final: 0.7609 (mt-10) REVERT: A 187 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6236 (pt0) REVERT: C 25 LYS cc_start: 0.7893 (mttt) cc_final: 0.7603 (ttmm) REVERT: C 51 ASP cc_start: 0.8751 (m-30) cc_final: 0.8409 (m-30) REVERT: C 66 MET cc_start: 0.8916 (mmm) cc_final: 0.8675 (mmt) REVERT: C 118 MET cc_start: 0.8694 (mtp) cc_final: 0.8423 (mtp) REVERT: C 154 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7538 (mtt90) REVERT: C 175 GLU cc_start: 0.7975 (tt0) cc_final: 0.7630 (mt-10) REVERT: C 197 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6167 (p0) REVERT: C 212 GLU cc_start: 0.7091 (tt0) cc_final: 0.6693 (tt0) REVERT: C 215 MET cc_start: 0.7846 (mtp) cc_final: 0.7543 (mtp) REVERT: E 25 LYS cc_start: 0.7863 (mttt) cc_final: 0.7559 (ttmm) REVERT: E 51 ASP cc_start: 0.8844 (m-30) cc_final: 0.8525 (m-30) REVERT: E 136 LEU cc_start: 0.8634 (mp) cc_final: 0.8415 (mt) REVERT: E 148 THR cc_start: 0.8044 (m) cc_final: 0.7770 (t) REVERT: E 175 GLU cc_start: 0.8064 (tt0) cc_final: 0.7701 (mt-10) REVERT: E 187 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6234 (pt0) REVERT: E 192 GLN cc_start: 0.7979 (tp40) cc_final: 0.7675 (tm-30) REVERT: E 197 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.6153 (p0) REVERT: G 18 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.6883 (ttt-90) REVERT: G 21 ASN cc_start: 0.8163 (t0) cc_final: 0.7808 (m110) REVERT: G 25 LYS cc_start: 0.8023 (mttt) cc_final: 0.7708 (ttmm) REVERT: G 145 TYR cc_start: 0.8298 (m-80) cc_final: 0.8046 (m-10) REVERT: G 148 THR cc_start: 0.7836 (m) cc_final: 0.7544 (t) REVERT: G 154 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7543 (mtp85) REVERT: G 175 GLU cc_start: 0.7845 (tt0) cc_final: 0.7588 (mt-10) REVERT: G 187 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6233 (pt0) REVERT: I 25 LYS cc_start: 0.7889 (mttt) cc_final: 0.7606 (ttmm) REVERT: I 51 ASP cc_start: 0.8734 (m-30) cc_final: 0.8387 (m-30) REVERT: I 66 MET cc_start: 0.8913 (mmm) cc_final: 0.8671 (mmt) REVERT: I 118 MET cc_start: 0.8708 (mtp) cc_final: 0.8435 (mtp) REVERT: I 154 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7524 (mtt90) REVERT: I 175 GLU cc_start: 0.7974 (tt0) cc_final: 0.7626 (mt-10) REVERT: I 197 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6192 (p0) REVERT: I 212 GLU cc_start: 0.7123 (tt0) cc_final: 0.6818 (tt0) REVERT: I 215 MET cc_start: 0.7839 (mtp) cc_final: 0.7530 (mtp) REVERT: K 18 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.6531 (ttt-90) REVERT: K 25 LYS cc_start: 0.7863 (mttt) cc_final: 0.7560 (ttmm) REVERT: K 51 ASP cc_start: 0.8843 (m-30) cc_final: 0.8526 (m-30) REVERT: K 136 LEU cc_start: 0.8637 (mp) cc_final: 0.8409 (mt) REVERT: K 148 THR cc_start: 0.8038 (m) cc_final: 0.7765 (t) REVERT: K 175 GLU cc_start: 0.8055 (tt0) cc_final: 0.7686 (mt-10) REVERT: K 187 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6212 (pt0) REVERT: K 192 GLN cc_start: 0.7971 (tp40) cc_final: 0.7667 (tm-30) REVERT: K 197 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6129 (p0) outliers start: 40 outliers final: 15 residues processed: 292 average time/residue: 0.6846 time to fit residues: 211.6843 Evaluate side-chains 295 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 179 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.155189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117975 restraints weight = 10497.826| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.35 r_work: 0.3228 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10566 Z= 0.115 Angle : 0.484 6.188 14364 Z= 0.237 Chirality : 0.041 0.152 1632 Planarity : 0.004 0.033 1854 Dihedral : 4.085 18.717 1410 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.72 % Allowed : 14.67 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.23), residues: 1308 helix: 1.98 (0.17), residues: 894 sheet: -0.55 (0.59), residues: 54 loop : 0.52 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 154 TYR 0.008 0.001 TYR C 145 PHE 0.010 0.002 PHE A 32 TRP 0.004 0.001 TRP K 117 HIS 0.002 0.000 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00279 (10566) covalent geometry : angle 0.48433 (14364) hydrogen bonds : bond 0.03189 ( 642) hydrogen bonds : angle 3.33364 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.373 Fit side-chains REVERT: A 18 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6697 (ttt-90) REVERT: A 21 ASN cc_start: 0.8105 (t0) cc_final: 0.7745 (m110) REVERT: A 25 LYS cc_start: 0.7910 (mttt) cc_final: 0.7637 (ttmm) REVERT: A 55 MET cc_start: 0.8579 (mtp) cc_final: 0.8273 (mtp) REVERT: A 145 TYR cc_start: 0.8238 (m-80) cc_final: 0.8023 (m-10) REVERT: A 148 THR cc_start: 0.7837 (m) cc_final: 0.7555 (t) REVERT: A 154 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7495 (mtp180) REVERT: A 175 GLU cc_start: 0.7861 (tt0) cc_final: 0.7619 (mt-10) REVERT: A 187 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6218 (pt0) REVERT: A 197 ASP cc_start: 0.6825 (OUTLIER) cc_final: 0.6124 (p0) REVERT: C 25 LYS cc_start: 0.7713 (mttt) cc_final: 0.7455 (ttmm) REVERT: C 30 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7383 (mtpp) REVERT: C 51 ASP cc_start: 0.8723 (m-30) cc_final: 0.8340 (m-30) REVERT: C 66 MET cc_start: 0.8905 (mmm) cc_final: 0.8693 (mmt) REVERT: C 118 MET cc_start: 0.8657 (mtp) cc_final: 0.8393 (mtp) REVERT: C 154 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7521 (mtt90) REVERT: C 175 GLU cc_start: 0.7808 (tt0) cc_final: 0.7471 (mt-10) REVERT: C 197 ASP cc_start: 0.6611 (OUTLIER) cc_final: 0.6037 (p0) REVERT: E 25 LYS cc_start: 0.7751 (mttt) cc_final: 0.7475 (ttmm) REVERT: E 51 ASP cc_start: 0.8792 (m-30) cc_final: 0.8394 (m-30) REVERT: E 136 LEU cc_start: 0.8559 (mp) cc_final: 0.8351 (mt) REVERT: E 175 GLU cc_start: 0.7914 (tt0) cc_final: 0.7536 (mt-10) REVERT: E 179 GLN cc_start: 0.8339 (tp40) cc_final: 0.7949 (tp-100) REVERT: E 187 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6149 (pt0) REVERT: E 192 GLN cc_start: 0.7908 (tp40) cc_final: 0.7614 (tm-30) REVERT: G 18 ARG cc_start: 0.7262 (ttp-170) cc_final: 0.6810 (ttt-90) REVERT: G 21 ASN cc_start: 0.8087 (t0) cc_final: 0.7734 (m110) REVERT: G 25 LYS cc_start: 0.7908 (mttt) cc_final: 0.7636 (ttmm) REVERT: G 55 MET cc_start: 0.8562 (mtp) cc_final: 0.8276 (mtp) REVERT: G 145 TYR cc_start: 0.8242 (m-80) cc_final: 0.8018 (m-10) REVERT: G 148 THR cc_start: 0.7839 (m) cc_final: 0.7555 (t) REVERT: G 154 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7489 (mtp180) REVERT: G 175 GLU cc_start: 0.7854 (tt0) cc_final: 0.7607 (mt-10) REVERT: G 187 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6213 (pt0) REVERT: G 197 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6104 (p0) REVERT: I 25 LYS cc_start: 0.7718 (mttt) cc_final: 0.7461 (ttmm) REVERT: I 30 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7405 (mtpp) REVERT: I 51 ASP cc_start: 0.8728 (m-30) cc_final: 0.8339 (m-30) REVERT: I 66 MET cc_start: 0.8892 (mmm) cc_final: 0.8674 (mmt) REVERT: I 118 MET cc_start: 0.8643 (mtp) cc_final: 0.8379 (mtp) REVERT: I 154 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7499 (mtt90) REVERT: I 175 GLU cc_start: 0.7785 (tt0) cc_final: 0.7446 (mt-10) REVERT: I 197 ASP cc_start: 0.6607 (OUTLIER) cc_final: 0.6034 (p0) REVERT: K 18 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.6451 (ttt-90) REVERT: K 25 LYS cc_start: 0.7760 (mttt) cc_final: 0.7481 (ttmm) REVERT: K 51 ASP cc_start: 0.8801 (m-30) cc_final: 0.8407 (m-30) REVERT: K 136 LEU cc_start: 0.8556 (mp) cc_final: 0.8342 (mt) REVERT: K 175 GLU cc_start: 0.7907 (tt0) cc_final: 0.7518 (mt-10) REVERT: K 179 GLN cc_start: 0.8347 (tp40) cc_final: 0.7962 (tp-100) REVERT: K 187 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6132 (pt0) REVERT: K 192 GLN cc_start: 0.7908 (tp40) cc_final: 0.7615 (tm-30) outliers start: 30 outliers final: 6 residues processed: 295 average time/residue: 0.6924 time to fit residues: 216.2871 Evaluate side-chains 288 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 276 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 64 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN C 112 GLN C 193 ASN C 219 GLN E 112 GLN I 112 GLN I 193 ASN I 219 GLN K 112 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117036 restraints weight = 10500.418| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.33 r_work: 0.3226 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10566 Z= 0.137 Angle : 0.490 6.498 14364 Z= 0.243 Chirality : 0.042 0.153 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.131 19.471 1410 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.17 % Allowed : 14.76 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.23), residues: 1308 helix: 1.97 (0.17), residues: 894 sheet: -0.73 (0.62), residues: 54 loop : 0.62 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 154 TYR 0.009 0.001 TYR K 145 PHE 0.011 0.002 PHE K 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00341 (10566) covalent geometry : angle 0.49007 (14364) hydrogen bonds : bond 0.03373 ( 642) hydrogen bonds : angle 3.35725 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.377 Fit side-chains REVERT: A 18 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6743 (ttt-90) REVERT: A 21 ASN cc_start: 0.8133 (t0) cc_final: 0.7765 (m110) REVERT: A 25 LYS cc_start: 0.7913 (mttt) cc_final: 0.7646 (ttmm) REVERT: A 145 TYR cc_start: 0.8300 (m-80) cc_final: 0.8081 (m-10) REVERT: A 154 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7473 (mtp85) REVERT: A 175 GLU cc_start: 0.7851 (tt0) cc_final: 0.7594 (mt-10) REVERT: A 187 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6246 (pt0) REVERT: A 197 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6189 (p0) REVERT: C 18 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.6695 (ttt-90) REVERT: C 25 LYS cc_start: 0.7820 (mttt) cc_final: 0.7524 (ttmm) REVERT: C 51 ASP cc_start: 0.8765 (m-30) cc_final: 0.8389 (m-30) REVERT: C 66 MET cc_start: 0.8899 (mmm) cc_final: 0.8695 (mmt) REVERT: C 68 MET cc_start: 0.8747 (mtm) cc_final: 0.8516 (mtm) REVERT: C 118 MET cc_start: 0.8694 (mtp) cc_final: 0.8422 (mtp) REVERT: C 154 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7494 (mtt90) REVERT: C 175 GLU cc_start: 0.7920 (tt0) cc_final: 0.7575 (mt-10) REVERT: C 197 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.6161 (p0) REVERT: C 212 GLU cc_start: 0.7307 (tt0) cc_final: 0.6825 (tt0) REVERT: C 215 MET cc_start: 0.7789 (mtp) cc_final: 0.7441 (mtp) REVERT: E 25 LYS cc_start: 0.7745 (mttt) cc_final: 0.7476 (ttmm) REVERT: E 51 ASP cc_start: 0.8829 (m-30) cc_final: 0.8409 (m-30) REVERT: E 79 GLU cc_start: 0.7897 (tp30) cc_final: 0.7630 (tp30) REVERT: E 136 LEU cc_start: 0.8600 (mp) cc_final: 0.8381 (mt) REVERT: E 175 GLU cc_start: 0.8024 (tt0) cc_final: 0.7670 (mt-10) REVERT: E 179 GLN cc_start: 0.8330 (tp40) cc_final: 0.7910 (tp-100) REVERT: E 187 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6156 (pt0) REVERT: E 192 GLN cc_start: 0.7936 (tp40) cc_final: 0.7649 (tm-30) REVERT: G 18 ARG cc_start: 0.7190 (ttp-170) cc_final: 0.6773 (ttt-90) REVERT: G 21 ASN cc_start: 0.8146 (t0) cc_final: 0.7783 (m110) REVERT: G 25 LYS cc_start: 0.7913 (mttt) cc_final: 0.7648 (ttmm) REVERT: G 145 TYR cc_start: 0.8305 (m-80) cc_final: 0.8084 (m-10) REVERT: G 154 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7480 (mtp85) REVERT: G 175 GLU cc_start: 0.7840 (tt0) cc_final: 0.7587 (mt-10) REVERT: G 187 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6248 (pt0) REVERT: G 197 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6157 (p0) REVERT: I 18 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6681 (ttt-90) REVERT: I 25 LYS cc_start: 0.7796 (mttt) cc_final: 0.7503 (ttmm) REVERT: I 51 ASP cc_start: 0.8770 (m-30) cc_final: 0.8393 (m-30) REVERT: I 66 MET cc_start: 0.8893 (mmm) cc_final: 0.8684 (mmt) REVERT: I 68 MET cc_start: 0.8730 (mtm) cc_final: 0.8497 (mtm) REVERT: I 118 MET cc_start: 0.8676 (mtp) cc_final: 0.8403 (mtp) REVERT: I 154 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7474 (mtt90) REVERT: I 175 GLU cc_start: 0.7919 (tt0) cc_final: 0.7568 (mt-10) REVERT: I 197 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6142 (p0) REVERT: I 212 GLU cc_start: 0.7337 (tt0) cc_final: 0.6858 (tt0) REVERT: I 215 MET cc_start: 0.7792 (mtp) cc_final: 0.7440 (mtp) REVERT: K 25 LYS cc_start: 0.7803 (mttt) cc_final: 0.7527 (ttmm) REVERT: K 51 ASP cc_start: 0.8853 (m-30) cc_final: 0.8436 (m-30) REVERT: K 79 GLU cc_start: 0.7885 (tp30) cc_final: 0.7615 (tp30) REVERT: K 136 LEU cc_start: 0.8590 (mp) cc_final: 0.8369 (mt) REVERT: K 175 GLU cc_start: 0.8022 (tt0) cc_final: 0.7661 (mt-10) REVERT: K 179 GLN cc_start: 0.8340 (tp40) cc_final: 0.7921 (tp-100) REVERT: K 187 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6150 (pt0) REVERT: K 192 GLN cc_start: 0.7944 (tp40) cc_final: 0.7657 (tm-30) outliers start: 35 outliers final: 14 residues processed: 290 average time/residue: 0.7077 time to fit residues: 217.1342 Evaluate side-chains 292 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114000 restraints weight = 10693.939| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.30 r_work: 0.3177 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10566 Z= 0.178 Angle : 0.526 7.129 14364 Z= 0.259 Chirality : 0.043 0.160 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.291 20.543 1410 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.44 % Allowed : 15.49 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.23), residues: 1308 helix: 1.77 (0.17), residues: 894 sheet: -0.70 (0.66), residues: 54 loop : 0.63 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.012 0.002 TYR K 169 PHE 0.012 0.002 PHE K 32 TRP 0.005 0.001 TRP A 80 HIS 0.003 0.001 HIS K 12 Details of bonding type rmsd covalent geometry : bond 0.00449 (10566) covalent geometry : angle 0.52555 (14364) hydrogen bonds : bond 0.03699 ( 642) hydrogen bonds : angle 3.46006 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 0.432 Fit side-chains REVERT: A 18 ARG cc_start: 0.7293 (ttp-170) cc_final: 0.6800 (ttt-90) REVERT: A 21 ASN cc_start: 0.8134 (t0) cc_final: 0.7756 (m110) REVERT: A 25 LYS cc_start: 0.7917 (mttt) cc_final: 0.7641 (ttmm) REVERT: A 145 TYR cc_start: 0.8303 (m-80) cc_final: 0.8102 (m-10) REVERT: A 154 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7449 (mtp85) REVERT: A 175 GLU cc_start: 0.7918 (tt0) cc_final: 0.7631 (mt-10) REVERT: A 187 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6199 (pt0) REVERT: A 197 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6229 (p0) REVERT: C 18 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6694 (ttt-90) REVERT: C 25 LYS cc_start: 0.7775 (mttt) cc_final: 0.7535 (ttmm) REVERT: C 51 ASP cc_start: 0.8799 (m-30) cc_final: 0.8444 (m-30) REVERT: C 118 MET cc_start: 0.8641 (mtp) cc_final: 0.8373 (mtp) REVERT: C 154 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7491 (mtt90) REVERT: C 175 GLU cc_start: 0.7922 (tt0) cc_final: 0.7586 (mt-10) REVERT: C 197 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6171 (p0) REVERT: E 25 LYS cc_start: 0.7810 (mttt) cc_final: 0.7569 (ttmm) REVERT: E 28 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7448 (mm-30) REVERT: E 51 ASP cc_start: 0.8827 (m-30) cc_final: 0.8344 (m-30) REVERT: E 79 GLU cc_start: 0.7841 (tp30) cc_final: 0.7607 (tp30) REVERT: E 175 GLU cc_start: 0.8104 (tt0) cc_final: 0.7752 (mt-10) REVERT: E 179 GLN cc_start: 0.8375 (tp40) cc_final: 0.7932 (tp-100) REVERT: E 187 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6169 (pt0) REVERT: E 192 GLN cc_start: 0.7956 (tp40) cc_final: 0.7660 (tm-30) REVERT: G 18 ARG cc_start: 0.7201 (ttp-170) cc_final: 0.6808 (ttt-90) REVERT: G 21 ASN cc_start: 0.8138 (t0) cc_final: 0.7769 (m110) REVERT: G 25 LYS cc_start: 0.7935 (mttt) cc_final: 0.7659 (ttmm) REVERT: G 145 TYR cc_start: 0.8302 (m-80) cc_final: 0.8098 (m-10) REVERT: G 154 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7449 (mtp85) REVERT: G 175 GLU cc_start: 0.7906 (tt0) cc_final: 0.7625 (mt-10) REVERT: G 187 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6214 (pt0) REVERT: G 197 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6222 (p0) REVERT: I 18 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6713 (ttt-90) REVERT: I 25 LYS cc_start: 0.7771 (mttt) cc_final: 0.7487 (ttmm) REVERT: I 51 ASP cc_start: 0.8796 (m-30) cc_final: 0.8443 (m-30) REVERT: I 66 MET cc_start: 0.8871 (mmm) cc_final: 0.8670 (mmt) REVERT: I 118 MET cc_start: 0.8625 (mtp) cc_final: 0.8363 (mtp) REVERT: I 154 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7478 (mtt90) REVERT: I 175 GLU cc_start: 0.7912 (tt0) cc_final: 0.7561 (mt-10) REVERT: I 197 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6171 (p0) REVERT: K 25 LYS cc_start: 0.7792 (mttt) cc_final: 0.7549 (ttmm) REVERT: K 28 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7439 (mm-30) REVERT: K 51 ASP cc_start: 0.8845 (m-30) cc_final: 0.8365 (m-30) REVERT: K 79 GLU cc_start: 0.7847 (tp30) cc_final: 0.7614 (tp30) REVERT: K 175 GLU cc_start: 0.8098 (tt0) cc_final: 0.7739 (mt-10) REVERT: K 179 GLN cc_start: 0.8383 (tp40) cc_final: 0.7943 (tp-100) REVERT: K 187 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6180 (pt0) REVERT: K 192 GLN cc_start: 0.7967 (tp40) cc_final: 0.7673 (tm-30) outliers start: 38 outliers final: 20 residues processed: 300 average time/residue: 0.6930 time to fit residues: 220.0732 Evaluate side-chains 305 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 113 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.151707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114596 restraints weight = 10499.443| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.30 r_work: 0.3203 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10566 Z= 0.148 Angle : 0.511 7.539 14364 Z= 0.252 Chirality : 0.043 0.181 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.207 19.644 1410 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.80 % Allowed : 15.58 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.23), residues: 1308 helix: 1.79 (0.17), residues: 894 sheet: -0.85 (0.68), residues: 54 loop : 0.59 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.011 0.002 TYR I 145 PHE 0.012 0.002 PHE E 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00372 (10566) covalent geometry : angle 0.51144 (14364) hydrogen bonds : bond 0.03466 ( 642) hydrogen bonds : angle 3.42285 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 282 time to evaluate : 0.400 Fit side-chains REVERT: A 18 ARG cc_start: 0.7281 (ttp-170) cc_final: 0.6800 (ttt-90) REVERT: A 21 ASN cc_start: 0.8146 (t0) cc_final: 0.7770 (m110) REVERT: A 25 LYS cc_start: 0.7908 (mttt) cc_final: 0.7639 (ttmm) REVERT: A 55 MET cc_start: 0.8632 (mtp) cc_final: 0.8313 (mtp) REVERT: A 145 TYR cc_start: 0.8290 (m-80) cc_final: 0.8069 (m-10) REVERT: A 154 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7475 (mtp180) REVERT: A 175 GLU cc_start: 0.7872 (tt0) cc_final: 0.7573 (mt-10) REVERT: A 187 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6262 (pt0) REVERT: A 197 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6217 (p0) REVERT: C 13 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: C 18 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6708 (ttt-90) REVERT: C 25 LYS cc_start: 0.7772 (mttt) cc_final: 0.7479 (ttmm) REVERT: C 51 ASP cc_start: 0.8787 (m-30) cc_final: 0.8395 (m-30) REVERT: C 68 MET cc_start: 0.8778 (mtm) cc_final: 0.8536 (mtm) REVERT: C 118 MET cc_start: 0.8665 (mtp) cc_final: 0.8426 (mtp) REVERT: C 154 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7528 (mtt90) REVERT: C 175 GLU cc_start: 0.7927 (tt0) cc_final: 0.7574 (mt-10) REVERT: C 197 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.6138 (p0) REVERT: E 25 LYS cc_start: 0.7831 (mttt) cc_final: 0.7586 (ttmm) REVERT: E 28 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7243 (mm-30) REVERT: E 51 ASP cc_start: 0.8828 (m-30) cc_final: 0.8371 (m-30) REVERT: E 79 GLU cc_start: 0.7854 (tp30) cc_final: 0.7629 (tp30) REVERT: E 136 LEU cc_start: 0.8612 (mp) cc_final: 0.8411 (mt) REVERT: E 140 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8385 (mtpm) REVERT: E 175 GLU cc_start: 0.8099 (tt0) cc_final: 0.7734 (mt-10) REVERT: E 179 GLN cc_start: 0.8378 (tp40) cc_final: 0.7959 (tp-100) REVERT: E 187 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6240 (pt0) REVERT: E 192 GLN cc_start: 0.7931 (tp40) cc_final: 0.7647 (tm-30) REVERT: G 18 ARG cc_start: 0.7187 (ttp-170) cc_final: 0.6809 (ttt-90) REVERT: G 21 ASN cc_start: 0.8136 (t0) cc_final: 0.7771 (m110) REVERT: G 25 LYS cc_start: 0.7935 (mttt) cc_final: 0.7666 (ttmm) REVERT: G 55 MET cc_start: 0.8631 (mtp) cc_final: 0.8314 (mtp) REVERT: G 145 TYR cc_start: 0.8288 (m-80) cc_final: 0.8088 (m-10) REVERT: G 154 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7480 (mtp180) REVERT: G 175 GLU cc_start: 0.7861 (tt0) cc_final: 0.7565 (mt-10) REVERT: G 187 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6263 (pt0) REVERT: G 197 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6220 (p0) REVERT: I 13 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: I 18 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6658 (ttt-90) REVERT: I 25 LYS cc_start: 0.7780 (mttt) cc_final: 0.7488 (ttmm) REVERT: I 51 ASP cc_start: 0.8795 (m-30) cc_final: 0.8407 (m-30) REVERT: I 68 MET cc_start: 0.8765 (mtm) cc_final: 0.8511 (mtm) REVERT: I 118 MET cc_start: 0.8653 (mtp) cc_final: 0.8416 (mtp) REVERT: I 154 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7510 (mtt90) REVERT: I 175 GLU cc_start: 0.7918 (tt0) cc_final: 0.7562 (mt-10) REVERT: I 197 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6125 (p0) REVERT: K 25 LYS cc_start: 0.7807 (mttt) cc_final: 0.7560 (ttmm) REVERT: K 28 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7233 (mm-30) REVERT: K 51 ASP cc_start: 0.8845 (m-30) cc_final: 0.8389 (m-30) REVERT: K 79 GLU cc_start: 0.7853 (tp30) cc_final: 0.7630 (tp30) REVERT: K 140 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8375 (mtpm) REVERT: K 175 GLU cc_start: 0.8090 (tt0) cc_final: 0.7715 (mt-10) REVERT: K 179 GLN cc_start: 0.8385 (tp40) cc_final: 0.7962 (tp-100) REVERT: K 187 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6233 (pt0) REVERT: K 192 GLN cc_start: 0.7953 (tp40) cc_final: 0.7671 (tm-30) outliers start: 42 outliers final: 25 residues processed: 291 average time/residue: 0.7007 time to fit residues: 215.6456 Evaluate side-chains 309 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 106 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117469 restraints weight = 10464.875| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.34 r_work: 0.3221 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10566 Z= 0.130 Angle : 0.497 7.590 14364 Z= 0.245 Chirality : 0.042 0.169 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.113 19.090 1410 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.71 % Allowed : 16.67 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.23), residues: 1308 helix: 1.88 (0.17), residues: 894 sheet: -0.96 (0.70), residues: 54 loop : 0.61 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.011 0.001 TYR I 145 PHE 0.011 0.002 PHE E 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00324 (10566) covalent geometry : angle 0.49671 (14364) hydrogen bonds : bond 0.03315 ( 642) hydrogen bonds : angle 3.36284 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.404 Fit side-chains REVERT: A 18 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.6714 (ttt-90) REVERT: A 21 ASN cc_start: 0.8070 (t0) cc_final: 0.7727 (m110) REVERT: A 25 LYS cc_start: 0.7870 (mttt) cc_final: 0.7603 (ttmm) REVERT: A 55 MET cc_start: 0.8629 (mtp) cc_final: 0.8304 (mtp) REVERT: A 145 TYR cc_start: 0.8275 (m-80) cc_final: 0.8020 (m-10) REVERT: A 154 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7456 (mtp180) REVERT: A 175 GLU cc_start: 0.7899 (tt0) cc_final: 0.7617 (mt-10) REVERT: A 187 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6112 (pt0) REVERT: A 197 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6184 (p0) REVERT: C 13 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: C 18 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6656 (ttt-90) REVERT: C 25 LYS cc_start: 0.7733 (mttt) cc_final: 0.7459 (ttmm) REVERT: C 51 ASP cc_start: 0.8759 (m-30) cc_final: 0.8369 (m-30) REVERT: C 68 MET cc_start: 0.8757 (mtm) cc_final: 0.8513 (mtm) REVERT: C 118 MET cc_start: 0.8690 (mtp) cc_final: 0.8464 (mtp) REVERT: C 154 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7509 (mtt90) REVERT: C 175 GLU cc_start: 0.7877 (tt0) cc_final: 0.7527 (mt-10) REVERT: E 25 LYS cc_start: 0.7782 (mttt) cc_final: 0.7538 (ttmm) REVERT: E 51 ASP cc_start: 0.8796 (m-30) cc_final: 0.8326 (m-30) REVERT: E 79 GLU cc_start: 0.7849 (tp30) cc_final: 0.7647 (tp30) REVERT: E 136 LEU cc_start: 0.8580 (mp) cc_final: 0.8373 (mt) REVERT: E 140 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8358 (mtpm) REVERT: E 175 GLU cc_start: 0.8038 (tt0) cc_final: 0.7683 (mt-10) REVERT: E 179 GLN cc_start: 0.8315 (tp40) cc_final: 0.7894 (tp-100) REVERT: E 187 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6178 (pt0) REVERT: E 192 GLN cc_start: 0.7908 (tp40) cc_final: 0.7636 (tm-30) REVERT: G 21 ASN cc_start: 0.8067 (t0) cc_final: 0.7741 (m110) REVERT: G 25 LYS cc_start: 0.7884 (mttt) cc_final: 0.7616 (ttmm) REVERT: G 55 MET cc_start: 0.8629 (mtp) cc_final: 0.8301 (mtp) REVERT: G 145 TYR cc_start: 0.8271 (m-80) cc_final: 0.8045 (m-10) REVERT: G 154 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7469 (mtp180) REVERT: G 175 GLU cc_start: 0.7898 (tt0) cc_final: 0.7617 (mt-10) REVERT: G 187 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6129 (pt0) REVERT: G 197 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6189 (p0) REVERT: I 13 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: I 18 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6766 (ttt-90) REVERT: I 25 LYS cc_start: 0.7716 (mttt) cc_final: 0.7437 (ttmm) REVERT: I 51 ASP cc_start: 0.8758 (m-30) cc_final: 0.8363 (m-30) REVERT: I 68 MET cc_start: 0.8742 (mtm) cc_final: 0.8494 (mtm) REVERT: I 118 MET cc_start: 0.8675 (mtp) cc_final: 0.8433 (mtp) REVERT: I 154 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7484 (mtt90) REVERT: I 175 GLU cc_start: 0.7859 (tt0) cc_final: 0.7509 (mt-10) REVERT: K 25 LYS cc_start: 0.7765 (mttt) cc_final: 0.7515 (ttmm) REVERT: K 51 ASP cc_start: 0.8812 (m-30) cc_final: 0.8346 (m-30) REVERT: K 79 GLU cc_start: 0.7855 (tp30) cc_final: 0.7653 (tp30) REVERT: K 140 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8344 (mtpm) REVERT: K 175 GLU cc_start: 0.8038 (tt0) cc_final: 0.7676 (mt-10) REVERT: K 179 GLN cc_start: 0.8309 (tp40) cc_final: 0.7884 (tp-100) REVERT: K 187 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6177 (pt0) REVERT: K 192 GLN cc_start: 0.7910 (tp40) cc_final: 0.7640 (tm-30) outliers start: 41 outliers final: 23 residues processed: 286 average time/residue: 0.7176 time to fit residues: 216.9542 Evaluate side-chains 297 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.155107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118070 restraints weight = 10467.551| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.33 r_work: 0.3221 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10566 Z= 0.129 Angle : 0.498 7.284 14364 Z= 0.247 Chirality : 0.042 0.160 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.087 18.985 1410 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.08 % Allowed : 17.75 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.23), residues: 1308 helix: 1.88 (0.17), residues: 894 sheet: -0.95 (0.72), residues: 54 loop : 0.61 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.011 0.001 TYR I 145 PHE 0.012 0.002 PHE K 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00319 (10566) covalent geometry : angle 0.49823 (14364) hydrogen bonds : bond 0.03295 ( 642) hydrogen bonds : angle 3.33877 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.443 Fit side-chains REVERT: A 15 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 18 ARG cc_start: 0.7184 (ttp-170) cc_final: 0.6705 (ttt-90) REVERT: A 21 ASN cc_start: 0.8103 (t0) cc_final: 0.7744 (m110) REVERT: A 25 LYS cc_start: 0.7899 (mttt) cc_final: 0.7639 (ttmm) REVERT: A 55 MET cc_start: 0.8631 (mtp) cc_final: 0.8311 (mtp) REVERT: A 145 TYR cc_start: 0.8255 (m-80) cc_final: 0.8003 (m-10) REVERT: A 154 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7451 (mtp180) REVERT: A 175 GLU cc_start: 0.7896 (tt0) cc_final: 0.7619 (mt-10) REVERT: A 187 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6093 (pt0) REVERT: A 197 ASP cc_start: 0.6822 (OUTLIER) cc_final: 0.6147 (p0) REVERT: C 13 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: C 18 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6664 (ttt-90) REVERT: C 25 LYS cc_start: 0.7661 (mttt) cc_final: 0.7403 (ttmm) REVERT: C 51 ASP cc_start: 0.8747 (m-30) cc_final: 0.8355 (m-30) REVERT: C 68 MET cc_start: 0.8733 (mtm) cc_final: 0.8488 (mtm) REVERT: C 118 MET cc_start: 0.8650 (mtp) cc_final: 0.8417 (mtp) REVERT: C 154 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7519 (mtt90) REVERT: C 175 GLU cc_start: 0.7901 (tt0) cc_final: 0.7551 (mt-10) REVERT: E 25 LYS cc_start: 0.7696 (mttt) cc_final: 0.7492 (ttmm) REVERT: E 28 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7307 (mm-30) REVERT: E 51 ASP cc_start: 0.8787 (m-30) cc_final: 0.8312 (m-30) REVERT: E 79 GLU cc_start: 0.7886 (tp30) cc_final: 0.7655 (tp30) REVERT: E 136 LEU cc_start: 0.8577 (mp) cc_final: 0.8363 (mt) REVERT: E 140 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8360 (mtpm) REVERT: E 175 GLU cc_start: 0.7989 (tt0) cc_final: 0.7628 (mt-10) REVERT: E 179 GLN cc_start: 0.8303 (tp40) cc_final: 0.7883 (tp-100) REVERT: E 187 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6175 (pt0) REVERT: E 192 GLN cc_start: 0.7890 (tp40) cc_final: 0.7626 (tm-30) REVERT: G 15 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8274 (mm) REVERT: G 21 ASN cc_start: 0.8094 (t0) cc_final: 0.7732 (m110) REVERT: G 25 LYS cc_start: 0.7905 (mttt) cc_final: 0.7643 (ttmm) REVERT: G 55 MET cc_start: 0.8632 (mtp) cc_final: 0.8310 (mtp) REVERT: G 145 TYR cc_start: 0.8268 (m-80) cc_final: 0.8031 (m-10) REVERT: G 154 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7459 (mtp180) REVERT: G 175 GLU cc_start: 0.7896 (tt0) cc_final: 0.7622 (mt-10) REVERT: G 187 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6114 (pt0) REVERT: G 197 ASP cc_start: 0.6811 (OUTLIER) cc_final: 0.6146 (p0) REVERT: I 13 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: I 18 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6768 (ttt-90) REVERT: I 25 LYS cc_start: 0.7658 (mttt) cc_final: 0.7395 (ttmm) REVERT: I 51 ASP cc_start: 0.8747 (m-30) cc_final: 0.8353 (m-30) REVERT: I 68 MET cc_start: 0.8736 (mtm) cc_final: 0.8492 (mtm) REVERT: I 118 MET cc_start: 0.8603 (mtp) cc_final: 0.8371 (mtp) REVERT: I 154 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7494 (mtt90) REVERT: I 175 GLU cc_start: 0.7885 (tt0) cc_final: 0.7531 (mt-10) REVERT: K 25 LYS cc_start: 0.7675 (mttt) cc_final: 0.7466 (ttmm) REVERT: K 28 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7303 (mm-30) REVERT: K 51 ASP cc_start: 0.8809 (m-30) cc_final: 0.8337 (m-30) REVERT: K 79 GLU cc_start: 0.7881 (tp30) cc_final: 0.7650 (tp30) REVERT: K 140 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8350 (mtpm) REVERT: K 175 GLU cc_start: 0.7987 (tt0) cc_final: 0.7617 (mt-10) REVERT: K 179 GLN cc_start: 0.8309 (tp40) cc_final: 0.7887 (tp-100) REVERT: K 187 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6165 (pt0) REVERT: K 192 GLN cc_start: 0.7891 (tp40) cc_final: 0.7627 (tm-30) outliers start: 34 outliers final: 17 residues processed: 275 average time/residue: 0.7287 time to fit residues: 211.7802 Evaluate side-chains 291 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 108 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 219 GLN E 112 GLN G 112 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118154 restraints weight = 10406.446| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.31 r_work: 0.3219 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10566 Z= 0.134 Angle : 0.508 7.635 14364 Z= 0.252 Chirality : 0.042 0.162 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.102 19.239 1410 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.63 % Allowed : 18.66 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.23), residues: 1308 helix: 1.87 (0.17), residues: 894 sheet: -0.86 (0.73), residues: 54 loop : 0.61 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 154 TYR 0.011 0.001 TYR C 145 PHE 0.012 0.002 PHE K 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00335 (10566) covalent geometry : angle 0.50785 (14364) hydrogen bonds : bond 0.03337 ( 642) hydrogen bonds : angle 3.32876 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.303 Fit side-chains REVERT: A 15 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8225 (mm) REVERT: A 18 ARG cc_start: 0.7196 (ttp-170) cc_final: 0.6720 (ttt-90) REVERT: A 21 ASN cc_start: 0.8135 (t0) cc_final: 0.7710 (m110) REVERT: A 25 LYS cc_start: 0.7864 (mttt) cc_final: 0.7637 (ttmm) REVERT: A 55 MET cc_start: 0.8639 (mtp) cc_final: 0.8287 (mtp) REVERT: A 145 TYR cc_start: 0.8270 (m-80) cc_final: 0.7994 (m-10) REVERT: A 154 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7449 (mtp180) REVERT: A 175 GLU cc_start: 0.7893 (tt0) cc_final: 0.7584 (mt-10) REVERT: A 187 GLU cc_start: 0.6651 (mt-10) cc_final: 0.6120 (pt0) REVERT: A 197 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6249 (p0) REVERT: C 13 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: C 18 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6669 (ttt-90) REVERT: C 25 LYS cc_start: 0.7656 (mttt) cc_final: 0.7399 (ttmm) REVERT: C 51 ASP cc_start: 0.8748 (m-30) cc_final: 0.8357 (m-30) REVERT: C 68 MET cc_start: 0.8727 (mtm) cc_final: 0.8482 (mtm) REVERT: C 118 MET cc_start: 0.8636 (mtp) cc_final: 0.8399 (mtp) REVERT: C 154 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7516 (mtt90) REVERT: C 175 GLU cc_start: 0.7860 (tt0) cc_final: 0.7522 (mt-10) REVERT: E 25 LYS cc_start: 0.7713 (mttt) cc_final: 0.7487 (ttmm) REVERT: E 26 VAL cc_start: 0.7839 (t) cc_final: 0.7604 (t) REVERT: E 28 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7138 (mm-30) REVERT: E 51 ASP cc_start: 0.8786 (m-30) cc_final: 0.8307 (m-30) REVERT: E 79 GLU cc_start: 0.7883 (tp30) cc_final: 0.7658 (tp30) REVERT: E 136 LEU cc_start: 0.8567 (mp) cc_final: 0.8360 (mt) REVERT: E 140 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8359 (mtpm) REVERT: E 175 GLU cc_start: 0.7986 (tt0) cc_final: 0.7632 (mt-10) REVERT: E 179 GLN cc_start: 0.8304 (tp40) cc_final: 0.7879 (tp-100) REVERT: E 187 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6172 (pt0) REVERT: E 192 GLN cc_start: 0.7889 (tp40) cc_final: 0.7625 (tm-30) REVERT: G 15 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8228 (mm) REVERT: G 21 ASN cc_start: 0.8130 (t0) cc_final: 0.7711 (m110) REVERT: G 25 LYS cc_start: 0.7873 (mttt) cc_final: 0.7644 (ttmm) REVERT: G 55 MET cc_start: 0.8634 (mtp) cc_final: 0.8279 (mtp) REVERT: G 145 TYR cc_start: 0.8297 (m-80) cc_final: 0.8031 (m-10) REVERT: G 154 ARG cc_start: 0.8079 (mtm-85) cc_final: 0.7456 (mtp180) REVERT: G 175 GLU cc_start: 0.7895 (tt0) cc_final: 0.7590 (mt-10) REVERT: G 187 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6131 (pt0) REVERT: G 197 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6240 (p0) REVERT: I 13 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: I 18 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6767 (ttt-90) REVERT: I 25 LYS cc_start: 0.7649 (mttt) cc_final: 0.7388 (ttmm) REVERT: I 51 ASP cc_start: 0.8750 (m-30) cc_final: 0.8356 (m-30) REVERT: I 68 MET cc_start: 0.8726 (mtm) cc_final: 0.8478 (mtm) REVERT: I 118 MET cc_start: 0.8621 (mtp) cc_final: 0.8386 (mtp) REVERT: I 154 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7496 (mtt90) REVERT: I 175 GLU cc_start: 0.7843 (tt0) cc_final: 0.7502 (mt-10) REVERT: K 25 LYS cc_start: 0.7689 (mttt) cc_final: 0.7461 (ttmm) REVERT: K 28 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7139 (mm-30) REVERT: K 51 ASP cc_start: 0.8811 (m-30) cc_final: 0.8379 (m-30) REVERT: K 79 GLU cc_start: 0.7888 (tp30) cc_final: 0.7660 (tp30) REVERT: K 140 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8349 (mtpm) REVERT: K 175 GLU cc_start: 0.7989 (tt0) cc_final: 0.7628 (mt-10) REVERT: K 179 GLN cc_start: 0.8308 (tp40) cc_final: 0.7881 (tp-100) REVERT: K 187 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6169 (pt0) REVERT: K 192 GLN cc_start: 0.7884 (tp40) cc_final: 0.7622 (tm-30) outliers start: 29 outliers final: 17 residues processed: 283 average time/residue: 0.7056 time to fit residues: 211.1220 Evaluate side-chains 299 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.0570 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 127 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN C 219 GLN E 112 GLN G 112 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116762 restraints weight = 10502.211| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.33 r_work: 0.3216 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10566 Z= 0.136 Angle : 0.506 7.626 14364 Z= 0.252 Chirality : 0.042 0.166 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.108 19.362 1410 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.99 % Allowed : 18.84 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.23), residues: 1308 helix: 1.87 (0.17), residues: 894 sheet: -0.79 (0.74), residues: 54 loop : 0.59 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.012 0.002 TYR C 145 PHE 0.012 0.002 PHE K 32 TRP 0.004 0.001 TRP C 23 HIS 0.002 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00338 (10566) covalent geometry : angle 0.50637 (14364) hydrogen bonds : bond 0.03339 ( 642) hydrogen bonds : angle 3.33116 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4681.03 seconds wall clock time: 80 minutes 6.83 seconds (4806.83 seconds total)