Starting phenix.real_space_refine on Mon Jul 28 10:17:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cky_16706/07_2025/8cky_16706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cky_16706/07_2025/8cky_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_16706/07_2025/8cky_16706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cky_16706/07_2025/8cky_16706.map" model { file = "/net/cci-nas-00/data/ceres_data/8cky_16706/07_2025/8cky_16706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cky_16706/07_2025/8cky_16706.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 1, 'ASN:plan1': 2} 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: D, F, H, J, L, C, E, G, I, K Time building chain proxies: 4.84, per 1000 atoms: 0.47 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: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.98 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: 3.01 Time building geometry restraints manager: 3.04 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: 0.08 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.830 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.018 0.005 TRP G 184 HIS 0.009 0.003 HIS I 12 PHE 0.013 0.003 PHE G 40 TYR 0.017 0.004 TYR E 169 ARG 0.015 0.002 ARG K 167 Details of bonding type rmsd hydrogen bonds : bond 0.11910 ( 642) hydrogen bonds : angle 5.65430 ( 1890) covalent geometry : bond 0.00423 (10566) covalent geometry : angle 0.81888 (14364) *********************** 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 : 1.082 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: 0.7870 (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: 0.6351 (pt0) REVERT: I 25 LYS cc_start: 0.8017 (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: 0.8213 (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: 0.8038 (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: 1.3501 time to fit residues: 500.6009 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 : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3739 r_free = 0.3739 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113544 restraints weight = 10464.990| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.30 r_work: 0.3240 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10566 Z= 0.188 Angle : 0.543 6.140 14364 Z= 0.277 Chirality : 0.043 0.136 1632 Planarity : 0.005 0.033 1854 Dihedral : 4.776 23.164 1410 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.71 % Allowed : 9.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1308 helix: 1.49 (0.17), residues: 894 sheet: -1.24 (0.46), residues: 54 loop : 0.56 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 184 HIS 0.003 0.001 HIS G 84 PHE 0.011 0.002 PHE E 161 TYR 0.009 0.001 TYR A 169 ARG 0.002 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 642) hydrogen bonds : angle 3.74981 ( 1890) covalent geometry : bond 0.00478 (10566) covalent geometry : angle 0.54291 (14364) *********************** 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 355 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 1.200 Fit side-chains REVERT: A 18 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.6993 (ttt-90) REVERT: A 21 ASN cc_start: 0.8191 (t0) cc_final: 0.7848 (m110) REVERT: A 25 LYS cc_start: 0.7911 (mttt) cc_final: 0.7620 (ttmm) REVERT: A 30 LYS cc_start: 0.7536 (mttt) cc_final: 0.7243 (mmtp) REVERT: A 145 TYR cc_start: 0.8314 (m-80) cc_final: 0.8079 (m-10) REVERT: A 154 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7516 (mtp180) REVERT: A 175 GLU cc_start: 0.7866 (tt0) cc_final: 0.7501 (mm-30) REVERT: A 187 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6384 (pt0) REVERT: C 25 LYS cc_start: 0.7995 (mttt) cc_final: 0.7694 (ttmm) REVERT: C 51 ASP cc_start: 0.8826 (m-30) cc_final: 0.8501 (m-30) REVERT: C 66 MET cc_start: 0.8937 (mmm) cc_final: 0.8694 (mmt) REVERT: C 118 MET cc_start: 0.8701 (mtp) cc_final: 0.8388 (mtp) REVERT: C 175 GLU cc_start: 0.8054 (tt0) cc_final: 0.7623 (mt-10) REVERT: C 185 MET cc_start: 0.8310 (mtm) cc_final: 0.7913 (mtt) REVERT: C 205 LEU cc_start: 0.7790 (mt) cc_final: 0.7576 (mp) REVERT: C 212 GLU cc_start: 0.7249 (tt0) cc_final: 0.6836 (tt0) REVERT: E 25 LYS cc_start: 0.7905 (mttt) cc_final: 0.7600 (ttmm) REVERT: E 136 LEU cc_start: 0.8734 (mp) cc_final: 0.8504 (mt) REVERT: E 175 GLU cc_start: 0.8054 (tt0) cc_final: 0.7694 (mt-10) REVERT: E 187 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6338 (pt0) REVERT: E 192 GLN cc_start: 0.7992 (tp40) cc_final: 0.7684 (tm-30) REVERT: G 18 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.6999 (ttt-90) REVERT: G 21 ASN cc_start: 0.8188 (t0) cc_final: 0.7850 (m110) REVERT: G 25 LYS cc_start: 0.7910 (mttt) cc_final: 0.7619 (ttmm) REVERT: G 30 LYS cc_start: 0.7525 (mttt) cc_final: 0.7235 (mmtp) REVERT: G 145 TYR cc_start: 0.8332 (m-80) cc_final: 0.8095 (m-10) REVERT: G 154 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7518 (mtp180) REVERT: G 175 GLU cc_start: 0.7834 (tt0) cc_final: 0.7458 (mm-30) REVERT: G 187 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6395 (pt0) REVERT: I 25 LYS cc_start: 0.7989 (mttt) cc_final: 0.7685 (ttmm) REVERT: I 51 ASP cc_start: 0.8817 (m-30) cc_final: 0.8484 (m-30) REVERT: I 66 MET cc_start: 0.8952 (mmm) cc_final: 0.8711 (mmt) REVERT: I 118 MET cc_start: 0.8712 (mtp) cc_final: 0.8393 (mtp) REVERT: I 175 GLU cc_start: 0.8048 (tt0) cc_final: 0.7619 (mt-10) REVERT: I 185 MET cc_start: 0.8307 (mtm) cc_final: 0.7907 (mtt) REVERT: I 205 LEU cc_start: 0.7800 (mt) cc_final: 0.7587 (mp) REVERT: I 212 GLU cc_start: 0.7273 (tt0) cc_final: 0.6863 (tt0) REVERT: K 25 LYS cc_start: 0.7900 (mttt) cc_final: 0.7596 (ttmm) REVERT: K 136 LEU cc_start: 0.8720 (mp) cc_final: 0.8485 (mt) REVERT: K 175 GLU cc_start: 0.8042 (tt0) cc_final: 0.7676 (mt-10) REVERT: K 187 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6322 (pt0) REVERT: K 192 GLN cc_start: 0.7976 (tp40) cc_final: 0.7667 (tm-30) outliers start: 52 outliers final: 16 residues processed: 313 average time/residue: 1.5471 time to fit residues: 513.9238 Evaluate side-chains 300 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 15 ILE 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 19 optimal weight: 0.0980 chunk 93 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 A 219 GLN C 112 GLN C 179 GLN C 192 GLN C 193 ASN C 219 GLN E 112 GLN G 50 GLN G 112 GLN G 193 ASN G 219 GLN I 112 GLN I 179 GLN I 192 GLN I 193 ASN I 219 GLN K 112 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116062 restraints weight = 10581.138| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.30 r_work: 0.3273 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10566 Z= 0.120 Angle : 0.479 6.455 14364 Z= 0.240 Chirality : 0.041 0.150 1632 Planarity : 0.004 0.033 1854 Dihedral : 4.197 19.325 1410 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.17 % Allowed : 13.50 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.22), residues: 1308 helix: 1.88 (0.17), residues: 894 sheet: -0.50 (0.56), residues: 54 loop : 0.49 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 117 HIS 0.001 0.000 HIS I 84 PHE 0.011 0.002 PHE K 32 TYR 0.006 0.001 TYR A 169 ARG 0.005 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 642) hydrogen bonds : angle 3.37268 ( 1890) covalent geometry : bond 0.00294 (10566) covalent geometry : angle 0.47914 (14364) *********************** 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 332 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 1.179 Fit side-chains REVERT: A 18 ARG cc_start: 0.7395 (ttp-170) cc_final: 0.6807 (ttt-90) REVERT: A 21 ASN cc_start: 0.8200 (t0) cc_final: 0.7856 (m110) REVERT: A 25 LYS cc_start: 0.8037 (mttt) cc_final: 0.7716 (ttmm) REVERT: A 148 THR cc_start: 0.7848 (m) cc_final: 0.7591 (t) REVERT: A 154 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7599 (mtp85) REVERT: A 175 GLU cc_start: 0.7847 (tt0) cc_final: 0.7627 (mt-10) REVERT: A 187 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6310 (pt0) REVERT: C 25 LYS cc_start: 0.7961 (mttt) cc_final: 0.7680 (ttmm) REVERT: C 51 ASP cc_start: 0.8756 (m-30) cc_final: 0.8401 (m-30) REVERT: C 66 MET cc_start: 0.8987 (mmm) cc_final: 0.8745 (mmt) REVERT: C 118 MET cc_start: 0.8712 (mtp) cc_final: 0.8450 (mtp) REVERT: C 154 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7556 (mtt90) REVERT: C 175 GLU cc_start: 0.7946 (tt0) cc_final: 0.7627 (mt-10) REVERT: C 197 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6203 (p0) REVERT: C 212 GLU cc_start: 0.7153 (tt0) cc_final: 0.6851 (tt0) REVERT: C 215 MET cc_start: 0.7899 (mtp) cc_final: 0.7619 (mtp) REVERT: E 25 LYS cc_start: 0.7948 (mttt) cc_final: 0.7614 (ttmm) REVERT: E 136 LEU cc_start: 0.8670 (mp) cc_final: 0.8450 (mt) REVERT: E 148 THR cc_start: 0.8026 (m) cc_final: 0.7814 (t) REVERT: E 175 GLU cc_start: 0.7985 (tt0) cc_final: 0.7670 (mt-10) REVERT: E 187 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6310 (pt0) REVERT: E 192 GLN cc_start: 0.7991 (tp40) cc_final: 0.7691 (tm-30) REVERT: E 197 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6120 (p0) REVERT: G 18 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.6959 (ttt-90) REVERT: G 21 ASN cc_start: 0.8203 (t0) cc_final: 0.7866 (m110) REVERT: G 25 LYS cc_start: 0.8080 (mttt) cc_final: 0.7760 (ttmm) REVERT: G 148 THR cc_start: 0.7866 (m) cc_final: 0.7609 (t) REVERT: G 154 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7603 (mtp85) REVERT: G 175 GLU cc_start: 0.7844 (tt0) cc_final: 0.7621 (mt-10) REVERT: G 187 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6288 (pt0) REVERT: I 25 LYS cc_start: 0.8006 (mttt) cc_final: 0.7760 (ttmm) REVERT: I 51 ASP cc_start: 0.8744 (m-30) cc_final: 0.8404 (m-30) REVERT: I 66 MET cc_start: 0.8976 (mmm) cc_final: 0.8729 (mmt) REVERT: I 118 MET cc_start: 0.8723 (mtp) cc_final: 0.8460 (mtp) REVERT: I 154 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7540 (mtt90) REVERT: I 175 GLU cc_start: 0.7957 (tt0) cc_final: 0.7635 (mt-10) REVERT: I 197 ASP cc_start: 0.6842 (OUTLIER) cc_final: 0.6233 (p0) REVERT: I 212 GLU cc_start: 0.7178 (tt0) cc_final: 0.6878 (tt0) REVERT: I 215 MET cc_start: 0.7885 (mtp) cc_final: 0.7602 (mtp) REVERT: K 18 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.6624 (ttt-90) REVERT: K 25 LYS cc_start: 0.7957 (mttt) cc_final: 0.7622 (ttmm) REVERT: K 136 LEU cc_start: 0.8661 (mp) cc_final: 0.8435 (mt) REVERT: K 148 THR cc_start: 0.8009 (m) cc_final: 0.7804 (t) REVERT: K 175 GLU cc_start: 0.7959 (tt0) cc_final: 0.7628 (mt-10) REVERT: K 187 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6270 (pt0) REVERT: K 192 GLN cc_start: 0.7978 (tp40) cc_final: 0.7678 (tm-30) REVERT: K 197 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6136 (p0) outliers start: 35 outliers final: 13 residues processed: 299 average time/residue: 1.4800 time to fit residues: 468.5755 Evaluate side-chains 296 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 279 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 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 101 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 219 GLN C 112 GLN C 219 GLN E 112 GLN E 179 GLN E 219 GLN G 112 GLN G 219 GLN I 112 GLN I 219 GLN K 112 GLN K 179 GLN K 219 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.153054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115596 restraints weight = 10380.202| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.33 r_work: 0.3201 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10566 Z= 0.163 Angle : 0.518 6.209 14364 Z= 0.257 Chirality : 0.043 0.164 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.319 20.710 1410 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.26 % Allowed : 14.86 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.22), residues: 1308 helix: 1.82 (0.17), residues: 894 sheet: -0.86 (0.57), residues: 54 loop : 0.47 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 80 HIS 0.002 0.001 HIS K 12 PHE 0.012 0.002 PHE E 32 TYR 0.009 0.002 TYR G 169 ARG 0.005 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 642) hydrogen bonds : angle 3.44713 ( 1890) covalent geometry : bond 0.00408 (10566) covalent geometry : angle 0.51833 (14364) *********************** 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 324 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 1.118 Fit side-chains REVERT: A 18 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6764 (ttt-90) REVERT: A 21 ASN cc_start: 0.8149 (t0) cc_final: 0.7765 (m110) REVERT: A 25 LYS cc_start: 0.7951 (mttt) cc_final: 0.7676 (ttmm) REVERT: A 51 ASP cc_start: 0.8762 (m-30) cc_final: 0.8554 (m-30) REVERT: A 154 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7468 (mtp85) REVERT: A 175 GLU cc_start: 0.7900 (tt0) cc_final: 0.7630 (mt-10) REVERT: A 187 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6246 (pt0) REVERT: A 197 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6640 (p0) REVERT: C 25 LYS cc_start: 0.7821 (mttt) cc_final: 0.7589 (ttmm) REVERT: C 51 ASP cc_start: 0.8802 (m-30) cc_final: 0.8466 (m-30) REVERT: C 66 MET cc_start: 0.8888 (mmm) cc_final: 0.8670 (mmt) REVERT: C 118 MET cc_start: 0.8666 (mtp) cc_final: 0.8386 (mtp) REVERT: C 154 ARG cc_start: 0.7981 (mtp85) cc_final: 0.7508 (mtt90) REVERT: C 175 GLU cc_start: 0.7908 (tt0) cc_final: 0.7551 (mt-10) REVERT: C 197 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6154 (p0) REVERT: E 25 LYS cc_start: 0.7848 (mttt) cc_final: 0.7544 (ttmm) REVERT: E 136 LEU cc_start: 0.8615 (mp) cc_final: 0.8399 (mt) REVERT: E 175 GLU cc_start: 0.8063 (tt0) cc_final: 0.7702 (mt-10) REVERT: E 179 GLN cc_start: 0.8364 (tp40) cc_final: 0.7989 (tp-100) REVERT: E 187 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6236 (pt0) REVERT: E 192 GLN cc_start: 0.7965 (tp40) cc_final: 0.7667 (tm-30) REVERT: G 18 ARG cc_start: 0.7402 (ttp-170) cc_final: 0.6926 (ttt-90) REVERT: G 21 ASN cc_start: 0.8140 (t0) cc_final: 0.7763 (m110) REVERT: G 25 LYS cc_start: 0.7938 (mttt) cc_final: 0.7664 (ttmm) REVERT: G 154 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7461 (mtp85) REVERT: G 175 GLU cc_start: 0.7879 (tt0) cc_final: 0.7610 (mt-10) REVERT: G 187 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6247 (pt0) REVERT: G 197 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6613 (p0) REVERT: I 25 LYS cc_start: 0.7805 (mttt) cc_final: 0.7578 (ttmm) REVERT: I 51 ASP cc_start: 0.8789 (m-30) cc_final: 0.8445 (m-30) REVERT: I 66 MET cc_start: 0.8876 (mmm) cc_final: 0.8658 (mmt) REVERT: I 118 MET cc_start: 0.8663 (mtp) cc_final: 0.8378 (mtp) REVERT: I 154 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7486 (mtt90) REVERT: I 175 GLU cc_start: 0.7902 (tt0) cc_final: 0.7538 (mt-10) REVERT: I 197 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6149 (p0) REVERT: K 18 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6472 (ttt-90) REVERT: K 25 LYS cc_start: 0.7828 (mttt) cc_final: 0.7528 (ttmm) REVERT: K 136 LEU cc_start: 0.8613 (mp) cc_final: 0.8388 (mt) REVERT: K 175 GLU cc_start: 0.8095 (tt0) cc_final: 0.7734 (mt-10) REVERT: K 179 GLN cc_start: 0.8365 (tp40) cc_final: 0.7990 (tp-100) REVERT: K 187 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6236 (pt0) REVERT: K 192 GLN cc_start: 0.7964 (tp40) cc_final: 0.7665 (tm-30) outliers start: 36 outliers final: 16 residues processed: 292 average time/residue: 1.5110 time to fit residues: 467.6884 Evaluate side-chains 298 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 15 ILE Chi-restraints excluded: chain C residue 33 SER 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 144 MET Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 33 SER 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 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 193 ASN C 219 GLN E 112 GLN G 219 GLN I 112 GLN I 193 ASN 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 = 0.3778 r_free = 0.3778 target = 0.154109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116859 restraints weight = 10408.426| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.33 r_work: 0.3232 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2819 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 : 0.504 6.720 14364 Z= 0.246 Chirality : 0.042 0.155 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.180 19.527 1410 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.08 % Allowed : 15.40 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.23), residues: 1308 helix: 1.85 (0.17), residues: 894 sheet: -0.75 (0.63), residues: 54 loop : 0.55 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 23 HIS 0.002 0.001 HIS E 12 PHE 0.011 0.002 PHE K 32 TYR 0.009 0.002 TYR E 145 ARG 0.006 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 642) hydrogen bonds : angle 3.38681 ( 1890) covalent geometry : bond 0.00340 (10566) covalent geometry : angle 0.50377 (14364) *********************** 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 326 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 1.258 Fit side-chains REVERT: A 18 ARG cc_start: 0.7220 (ttp-170) cc_final: 0.6704 (ttt-90) REVERT: A 21 ASN cc_start: 0.8140 (t0) cc_final: 0.7779 (m110) REVERT: A 25 LYS cc_start: 0.7934 (mttt) cc_final: 0.7657 (ttmm) REVERT: A 55 MET cc_start: 0.8620 (mtp) cc_final: 0.8287 (mtp) REVERT: A 154 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7483 (mtp180) REVERT: A 175 GLU cc_start: 0.7891 (tt0) cc_final: 0.7647 (mt-10) REVERT: A 187 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6237 (pt0) REVERT: A 197 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6209 (p0) REVERT: C 18 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.6657 (mtt-85) REVERT: C 25 LYS cc_start: 0.7767 (mttt) cc_final: 0.7468 (ttmm) REVERT: C 51 ASP cc_start: 0.8769 (m-30) cc_final: 0.8387 (m-30) REVERT: C 66 MET cc_start: 0.8903 (mmm) cc_final: 0.8690 (mmt) REVERT: C 118 MET cc_start: 0.8701 (mtp) cc_final: 0.8458 (mtp) REVERT: C 154 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7438 (mtt90) REVERT: C 175 GLU cc_start: 0.7873 (tt0) cc_final: 0.7540 (mt-10) REVERT: C 197 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6096 (p0) REVERT: E 25 LYS cc_start: 0.7792 (mttt) cc_final: 0.7499 (ttmm) REVERT: E 51 ASP cc_start: 0.8814 (m-30) cc_final: 0.8473 (m-30) REVERT: E 136 LEU cc_start: 0.8601 (mp) cc_final: 0.8398 (mt) REVERT: E 175 GLU cc_start: 0.8041 (tt0) cc_final: 0.7709 (mt-10) REVERT: E 187 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6234 (pt0) REVERT: E 192 GLN cc_start: 0.7956 (tp40) cc_final: 0.7675 (tm-30) REVERT: G 18 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6883 (ttt-90) REVERT: G 21 ASN cc_start: 0.8112 (t0) cc_final: 0.7760 (m110) REVERT: G 25 LYS cc_start: 0.7928 (mttt) cc_final: 0.7652 (ttmm) REVERT: G 51 ASP cc_start: 0.8856 (m-30) cc_final: 0.8433 (m-30) REVERT: G 55 MET cc_start: 0.8647 (mtp) cc_final: 0.8318 (mtp) REVERT: G 154 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7495 (mtp180) REVERT: G 175 GLU cc_start: 0.7870 (tt0) cc_final: 0.7631 (mt-10) REVERT: G 187 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6232 (pt0) REVERT: G 197 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.6175 (p0) REVERT: I 25 LYS cc_start: 0.7778 (mttt) cc_final: 0.7477 (ttmm) REVERT: I 51 ASP cc_start: 0.8766 (m-30) cc_final: 0.8384 (m-30) REVERT: I 66 MET cc_start: 0.8889 (mmm) cc_final: 0.8672 (mmt) REVERT: I 118 MET cc_start: 0.8689 (mtp) cc_final: 0.8447 (mtp) REVERT: I 154 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7419 (mtt90) REVERT: I 175 GLU cc_start: 0.7878 (tt0) cc_final: 0.7533 (mt-10) REVERT: I 197 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6095 (p0) REVERT: K 25 LYS cc_start: 0.7773 (mttt) cc_final: 0.7479 (ttmm) REVERT: K 51 ASP cc_start: 0.8850 (m-30) cc_final: 0.8532 (m-30) REVERT: K 136 LEU cc_start: 0.8591 (mp) cc_final: 0.8381 (mt) REVERT: K 175 GLU cc_start: 0.8035 (tt0) cc_final: 0.7690 (mt-10) REVERT: K 187 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6238 (pt0) REVERT: K 192 GLN cc_start: 0.7945 (tp40) cc_final: 0.7663 (tm-30) outliers start: 34 outliers final: 16 residues processed: 300 average time/residue: 1.5778 time to fit residues: 503.7563 Evaluate side-chains 290 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 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 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 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 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.151165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114181 restraints weight = 10550.993| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.31 r_work: 0.3206 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10566 Z= 0.165 Angle : 0.510 6.701 14364 Z= 0.255 Chirality : 0.043 0.172 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.296 20.336 1410 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.26 % Allowed : 16.49 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1308 helix: 1.76 (0.17), residues: 894 sheet: -0.69 (0.66), residues: 54 loop : 0.58 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 80 HIS 0.002 0.001 HIS K 12 PHE 0.012 0.002 PHE K 32 TYR 0.011 0.002 TYR K 145 ARG 0.006 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 642) hydrogen bonds : angle 3.45450 ( 1890) covalent geometry : bond 0.00417 (10566) covalent geometry : angle 0.51044 (14364) *********************** 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 324 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 1.248 Fit side-chains REVERT: A 18 ARG cc_start: 0.7302 (ttp-170) cc_final: 0.6808 (ttt-90) REVERT: A 21 ASN cc_start: 0.8152 (t0) cc_final: 0.7773 (m110) REVERT: A 25 LYS cc_start: 0.7945 (mttt) cc_final: 0.7665 (ttmm) REVERT: A 154 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7479 (mtp180) REVERT: A 175 GLU cc_start: 0.7879 (tt0) cc_final: 0.7583 (mt-10) REVERT: A 187 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6209 (pt0) REVERT: A 197 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6300 (p0) REVERT: C 18 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6668 (ttt-90) REVERT: C 25 LYS cc_start: 0.7797 (mttt) cc_final: 0.7497 (ttmm) REVERT: C 51 ASP cc_start: 0.8793 (m-30) cc_final: 0.8444 (m-30) REVERT: C 68 MET cc_start: 0.8747 (mtm) cc_final: 0.8511 (mtm) REVERT: C 118 MET cc_start: 0.8659 (mtp) cc_final: 0.8404 (mtp) REVERT: C 154 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7510 (mtt90) REVERT: C 175 GLU cc_start: 0.7916 (tt0) cc_final: 0.7591 (mt-10) REVERT: C 197 ASP cc_start: 0.6736 (OUTLIER) cc_final: 0.6166 (p0) REVERT: C 215 MET cc_start: 0.7862 (mtp) cc_final: 0.7608 (mtp) REVERT: E 25 LYS cc_start: 0.7800 (mttt) cc_final: 0.7511 (ttmm) REVERT: E 28 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7451 (mm-30) REVERT: E 51 ASP cc_start: 0.8817 (m-30) cc_final: 0.8423 (m-30) REVERT: E 175 GLU cc_start: 0.8074 (tt0) cc_final: 0.7733 (mt-10) REVERT: E 187 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6250 (pt0) REVERT: E 192 GLN cc_start: 0.7976 (tp40) cc_final: 0.7693 (tm-30) REVERT: G 18 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6824 (ttt-90) REVERT: G 21 ASN cc_start: 0.8138 (t0) cc_final: 0.7769 (m110) REVERT: G 25 LYS cc_start: 0.7945 (mttt) cc_final: 0.7666 (ttmm) REVERT: G 51 ASP cc_start: 0.8834 (m-30) cc_final: 0.8421 (m-30) REVERT: G 154 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7479 (mtp180) REVERT: G 175 GLU cc_start: 0.7868 (tt0) cc_final: 0.7574 (mt-10) REVERT: G 187 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6210 (pt0) REVERT: G 197 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6280 (p0) REVERT: I 18 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.6772 (mtt-85) REVERT: I 25 LYS cc_start: 0.7812 (mttt) cc_final: 0.7515 (ttmm) REVERT: I 51 ASP cc_start: 0.8800 (m-30) cc_final: 0.8455 (m-30) REVERT: I 68 MET cc_start: 0.8733 (mtm) cc_final: 0.8494 (mtm) REVERT: I 118 MET cc_start: 0.8636 (mtp) cc_final: 0.8386 (mtp) REVERT: I 154 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7507 (mtt90) REVERT: I 175 GLU cc_start: 0.7920 (tt0) cc_final: 0.7590 (mt-10) REVERT: I 197 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6157 (p0) REVERT: I 215 MET cc_start: 0.7851 (mtp) cc_final: 0.7591 (mtp) REVERT: K 25 LYS cc_start: 0.7783 (mttt) cc_final: 0.7494 (ttmm) REVERT: K 28 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7463 (mm-30) REVERT: K 51 ASP cc_start: 0.8844 (m-30) cc_final: 0.8470 (m-30) REVERT: K 175 GLU cc_start: 0.8070 (tt0) cc_final: 0.7725 (mt-10) REVERT: K 187 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6258 (pt0) REVERT: K 192 GLN cc_start: 0.7980 (tp40) cc_final: 0.7697 (tm-30) outliers start: 36 outliers final: 22 residues processed: 296 average time/residue: 1.4628 time to fit residues: 458.7716 Evaluate side-chains 306 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 172 LEU 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 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 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 172 LEU 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 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 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3769 r_free = 0.3769 target = 0.152911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116224 restraints weight = 10576.511| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.28 r_work: 0.3199 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10566 Z= 0.154 Angle : 0.525 7.628 14364 Z= 0.257 Chirality : 0.043 0.181 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.253 19.916 1410 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.44 % Allowed : 17.03 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1308 helix: 1.75 (0.17), residues: 894 sheet: -0.87 (0.67), residues: 54 loop : 0.59 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 80 HIS 0.002 0.001 HIS K 12 PHE 0.012 0.002 PHE E 32 TYR 0.011 0.002 TYR E 145 ARG 0.007 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 642) hydrogen bonds : angle 3.40620 ( 1890) covalent geometry : bond 0.00386 (10566) covalent geometry : angle 0.52457 (14364) *********************** 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 321 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 1.094 Fit side-chains REVERT: A 18 ARG cc_start: 0.7206 (ttp-170) cc_final: 0.6725 (ttt-90) REVERT: A 21 ASN cc_start: 0.8101 (t0) cc_final: 0.7723 (m110) REVERT: A 25 LYS cc_start: 0.7854 (mttt) cc_final: 0.7577 (ttmm) REVERT: A 154 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7438 (mtp180) REVERT: A 175 GLU cc_start: 0.7847 (tt0) cc_final: 0.7535 (mt-10) REVERT: A 187 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6200 (pt0) REVERT: A 197 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6242 (p0) REVERT: C 18 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.6644 (ttt-90) REVERT: C 25 LYS cc_start: 0.7676 (mttt) cc_final: 0.7390 (ttmm) REVERT: C 51 ASP cc_start: 0.8759 (m-30) cc_final: 0.8374 (m-30) REVERT: C 118 MET cc_start: 0.8615 (mtp) cc_final: 0.8378 (mtp) REVERT: C 154 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7482 (mtt90) REVERT: C 175 GLU cc_start: 0.7908 (tt0) cc_final: 0.7542 (mt-10) REVERT: C 197 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6116 (p0) REVERT: E 25 LYS cc_start: 0.7731 (mttt) cc_final: 0.7446 (ttmm) REVERT: E 28 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7232 (mm-30) REVERT: E 51 ASP cc_start: 0.8802 (m-30) cc_final: 0.8384 (m-30) REVERT: E 175 GLU cc_start: 0.8041 (tt0) cc_final: 0.7684 (mt-10) REVERT: E 187 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6140 (pt0) REVERT: E 192 GLN cc_start: 0.7919 (tp40) cc_final: 0.7634 (tm-30) REVERT: G 18 ARG cc_start: 0.7164 (ttp-170) cc_final: 0.6713 (ttt-90) REVERT: G 21 ASN cc_start: 0.8088 (t0) cc_final: 0.7718 (m110) REVERT: G 25 LYS cc_start: 0.7859 (mttt) cc_final: 0.7582 (ttmm) REVERT: G 51 ASP cc_start: 0.8804 (m-30) cc_final: 0.8372 (m-30) REVERT: G 154 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7438 (mtp180) REVERT: G 175 GLU cc_start: 0.7820 (tt0) cc_final: 0.7511 (mt-10) REVERT: G 187 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6195 (pt0) REVERT: G 197 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6225 (p0) REVERT: I 18 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.6752 (mtt-85) REVERT: I 25 LYS cc_start: 0.7692 (mttt) cc_final: 0.7400 (ttmm) REVERT: I 51 ASP cc_start: 0.8760 (m-30) cc_final: 0.8375 (m-30) REVERT: I 118 MET cc_start: 0.8598 (mtp) cc_final: 0.8365 (mtp) REVERT: I 154 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7481 (mtt90) REVERT: I 175 GLU cc_start: 0.7896 (tt0) cc_final: 0.7532 (mt-10) REVERT: I 197 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6102 (p0) REVERT: K 25 LYS cc_start: 0.7704 (mttt) cc_final: 0.7413 (ttmm) REVERT: K 51 ASP cc_start: 0.8823 (m-30) cc_final: 0.8425 (m-30) REVERT: K 175 GLU cc_start: 0.8041 (tt0) cc_final: 0.7680 (mt-10) REVERT: K 187 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6154 (pt0) REVERT: K 192 GLN cc_start: 0.7947 (tp40) cc_final: 0.7664 (tm-30) outliers start: 38 outliers final: 26 residues processed: 292 average time/residue: 1.4779 time to fit residues: 456.7771 Evaluate side-chains 309 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 279 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 172 LEU 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 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 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 172 LEU 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 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 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 64 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.152136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115004 restraints weight = 10560.089| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.31 r_work: 0.3202 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2918 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= 0.147 Angle : 0.504 7.195 14364 Z= 0.253 Chirality : 0.043 0.168 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.232 19.742 1410 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.44 % Allowed : 16.85 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1308 helix: 1.76 (0.17), residues: 894 sheet: -0.88 (0.71), residues: 54 loop : 0.63 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 80 HIS 0.002 0.001 HIS K 12 PHE 0.012 0.002 PHE K 32 TYR 0.011 0.002 TYR E 145 ARG 0.007 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 642) hydrogen bonds : angle 3.38383 ( 1890) covalent geometry : bond 0.00368 (10566) covalent geometry : angle 0.50411 (14364) *********************** 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 316 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 1.184 Fit side-chains REVERT: A 18 ARG cc_start: 0.7172 (ttp-170) cc_final: 0.6747 (ttt-90) REVERT: A 21 ASN cc_start: 0.8152 (t0) cc_final: 0.7782 (m110) REVERT: A 25 LYS cc_start: 0.7920 (mttt) cc_final: 0.7645 (ttmm) REVERT: A 154 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7474 (mtp180) REVERT: A 175 GLU cc_start: 0.7914 (tt0) cc_final: 0.7592 (mt-10) REVERT: A 187 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6221 (pt0) REVERT: A 197 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6258 (p0) REVERT: C 18 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6674 (mtt-85) REVERT: C 25 LYS cc_start: 0.7722 (mttt) cc_final: 0.7451 (ttmm) REVERT: C 51 ASP cc_start: 0.8777 (m-30) cc_final: 0.8392 (m-30) REVERT: C 68 MET cc_start: 0.8789 (mtm) cc_final: 0.8519 (mtm) REVERT: C 118 MET cc_start: 0.8671 (mtp) cc_final: 0.8444 (mtp) REVERT: C 154 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7522 (mtt90) REVERT: C 175 GLU cc_start: 0.7895 (tt0) cc_final: 0.7537 (mt-10) REVERT: E 25 LYS cc_start: 0.7765 (mttt) cc_final: 0.7530 (ttmm) REVERT: E 51 ASP cc_start: 0.8825 (m-30) cc_final: 0.8373 (m-30) REVERT: E 175 GLU cc_start: 0.8058 (tt0) cc_final: 0.7715 (mt-10) REVERT: E 187 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6215 (pt0) REVERT: E 192 GLN cc_start: 0.7913 (tp40) cc_final: 0.7637 (tm-30) REVERT: G 18 ARG cc_start: 0.7189 (ttp-170) cc_final: 0.6764 (ttt-90) REVERT: G 21 ASN cc_start: 0.8127 (t0) cc_final: 0.7763 (m110) REVERT: G 25 LYS cc_start: 0.7903 (mttt) cc_final: 0.7633 (ttmm) REVERT: G 51 ASP cc_start: 0.8804 (m-30) cc_final: 0.8332 (m-30) REVERT: G 55 MET cc_start: 0.8601 (mtp) cc_final: 0.8280 (mtp) REVERT: G 154 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7466 (mtp180) REVERT: G 175 GLU cc_start: 0.7898 (tt0) cc_final: 0.7578 (mt-10) REVERT: G 187 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6237 (pt0) REVERT: G 197 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6223 (p0) REVERT: I 18 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6776 (mtt-85) REVERT: I 25 LYS cc_start: 0.7701 (mttt) cc_final: 0.7432 (ttmm) REVERT: I 51 ASP cc_start: 0.8792 (m-30) cc_final: 0.8413 (m-30) REVERT: I 68 MET cc_start: 0.8781 (mtm) cc_final: 0.8507 (mtm) REVERT: I 118 MET cc_start: 0.8655 (mtp) cc_final: 0.8431 (mtp) REVERT: I 154 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7511 (mtt90) REVERT: I 175 GLU cc_start: 0.7894 (tt0) cc_final: 0.7536 (mt-10) REVERT: K 25 LYS cc_start: 0.7743 (mttt) cc_final: 0.7483 (ttmm) REVERT: K 51 ASP cc_start: 0.8823 (m-30) cc_final: 0.8428 (m-30) REVERT: K 175 GLU cc_start: 0.8057 (tt0) cc_final: 0.7708 (mt-10) REVERT: K 187 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6227 (pt0) REVERT: K 192 GLN cc_start: 0.7935 (tp40) cc_final: 0.7662 (tm-30) outliers start: 38 outliers final: 25 residues processed: 287 average time/residue: 1.7605 time to fit residues: 533.9482 Evaluate side-chains 301 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 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 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 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 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 54 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3760 r_free = 0.3760 target = 0.151911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114666 restraints weight = 10630.296| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.32 r_work: 0.3195 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10566 Z= 0.157 Angle : 0.527 7.885 14364 Z= 0.262 Chirality : 0.043 0.168 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.264 19.975 1410 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.26 % Allowed : 17.84 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1308 helix: 1.73 (0.17), residues: 894 sheet: -0.68 (0.74), residues: 54 loop : 0.63 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 80 HIS 0.002 0.001 HIS A 12 PHE 0.013 0.002 PHE E 32 TYR 0.012 0.002 TYR E 145 ARG 0.007 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 642) hydrogen bonds : angle 3.39509 ( 1890) covalent geometry : bond 0.00393 (10566) covalent geometry : angle 0.52724 (14364) *********************** 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 314 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.308 Fit side-chains REVERT: A 18 ARG cc_start: 0.7237 (ttp-170) cc_final: 0.6797 (ttt-90) REVERT: A 21 ASN cc_start: 0.8123 (t0) cc_final: 0.7766 (m110) REVERT: A 25 LYS cc_start: 0.7905 (mttt) cc_final: 0.7655 (ttmm) REVERT: A 154 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7481 (mtp180) REVERT: A 175 GLU cc_start: 0.7908 (tt0) cc_final: 0.7583 (mt-10) REVERT: A 187 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6210 (pt0) REVERT: A 197 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6256 (p0) REVERT: C 13 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: C 18 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6687 (mtt-85) REVERT: C 25 LYS cc_start: 0.7715 (mttt) cc_final: 0.7441 (ttmm) REVERT: C 51 ASP cc_start: 0.8790 (m-30) cc_final: 0.8417 (m-30) REVERT: C 68 MET cc_start: 0.8769 (mtm) cc_final: 0.8508 (mtm) REVERT: C 118 MET cc_start: 0.8654 (mtp) cc_final: 0.8421 (mtp) REVERT: C 154 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7519 (mtt90) REVERT: C 175 GLU cc_start: 0.7911 (tt0) cc_final: 0.7570 (mt-10) REVERT: E 25 LYS cc_start: 0.7839 (mttt) cc_final: 0.7586 (ttmm) REVERT: E 28 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7344 (mm-30) REVERT: E 51 ASP cc_start: 0.8821 (m-30) cc_final: 0.8358 (m-30) REVERT: E 175 GLU cc_start: 0.8061 (tt0) cc_final: 0.7714 (mt-10) REVERT: E 187 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6166 (pt0) REVERT: E 192 GLN cc_start: 0.7932 (tp40) cc_final: 0.7656 (tm-30) REVERT: G 18 ARG cc_start: 0.7256 (ttp-170) cc_final: 0.6774 (ttt-90) REVERT: G 21 ASN cc_start: 0.8093 (t0) cc_final: 0.7742 (m110) REVERT: G 25 LYS cc_start: 0.7889 (mttt) cc_final: 0.7635 (ttmm) REVERT: G 51 ASP cc_start: 0.8800 (m-30) cc_final: 0.8320 (m-30) REVERT: G 55 MET cc_start: 0.8651 (mtp) cc_final: 0.8314 (mtp) REVERT: G 154 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7459 (mtp180) REVERT: G 175 GLU cc_start: 0.7906 (tt0) cc_final: 0.7584 (mt-10) REVERT: G 187 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6224 (pt0) REVERT: G 197 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6234 (p0) REVERT: I 13 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: I 18 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6802 (ttt-90) REVERT: I 25 LYS cc_start: 0.7698 (mttt) cc_final: 0.7428 (ttmm) REVERT: I 51 ASP cc_start: 0.8781 (m-30) cc_final: 0.8399 (m-30) REVERT: I 68 MET cc_start: 0.8757 (mtm) cc_final: 0.8493 (mtm) REVERT: I 118 MET cc_start: 0.8636 (mtp) cc_final: 0.8408 (mtp) REVERT: I 154 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7511 (mtt90) REVERT: I 175 GLU cc_start: 0.7914 (tt0) cc_final: 0.7567 (mt-10) REVERT: K 25 LYS cc_start: 0.7754 (mttt) cc_final: 0.7481 (ttmm) REVERT: K 28 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7387 (mm-30) REVERT: K 51 ASP cc_start: 0.8830 (m-30) cc_final: 0.8427 (m-30) REVERT: K 175 GLU cc_start: 0.8062 (tt0) cc_final: 0.7714 (mt-10) REVERT: K 187 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6180 (pt0) REVERT: K 192 GLN cc_start: 0.7948 (tp40) cc_final: 0.7673 (tm-30) outliers start: 36 outliers final: 24 residues processed: 285 average time/residue: 1.5385 time to fit residues: 463.3448 Evaluate side-chains 304 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 SER 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 102 SER 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 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 102 SER 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 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.154083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117040 restraints weight = 10488.705| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.30 r_work: 0.3199 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10566 Z= 0.165 Angle : 0.525 7.609 14364 Z= 0.264 Chirality : 0.043 0.172 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.304 20.155 1410 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.26 % Allowed : 18.12 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1308 helix: 1.68 (0.17), residues: 894 sheet: -0.61 (0.74), residues: 54 loop : 0.59 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 80 HIS 0.003 0.001 HIS K 12 PHE 0.013 0.002 PHE E 32 TYR 0.012 0.002 TYR K 145 ARG 0.007 0.000 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 642) hydrogen bonds : angle 3.40393 ( 1890) covalent geometry : bond 0.00416 (10566) covalent geometry : angle 0.52510 (14364) ********************** 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 310 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 1.423 Fit side-chains REVERT: A 18 ARG cc_start: 0.7255 (ttp-170) cc_final: 0.6747 (ttt-90) REVERT: A 21 ASN cc_start: 0.8114 (t0) cc_final: 0.7690 (m110) REVERT: A 25 LYS cc_start: 0.7859 (mttt) cc_final: 0.7580 (ttmm) REVERT: A 154 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7433 (mtp180) REVERT: A 175 GLU cc_start: 0.7840 (tt0) cc_final: 0.7548 (mt-10) REVERT: A 187 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6181 (pt0) REVERT: A 197 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6233 (p0) REVERT: C 13 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: C 18 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6702 (mtt-85) REVERT: C 25 LYS cc_start: 0.7665 (mttt) cc_final: 0.7388 (ttmm) REVERT: C 51 ASP cc_start: 0.8769 (m-30) cc_final: 0.8379 (m-30) REVERT: C 68 MET cc_start: 0.8708 (mtm) cc_final: 0.8462 (mtm) REVERT: C 118 MET cc_start: 0.8596 (mtp) cc_final: 0.8357 (mtp) REVERT: C 154 ARG cc_start: 0.7925 (mtp85) cc_final: 0.7476 (mtt90) REVERT: C 175 GLU cc_start: 0.7900 (tt0) cc_final: 0.7534 (mt-10) REVERT: E 25 LYS cc_start: 0.7730 (mttt) cc_final: 0.7446 (ttmm) REVERT: E 28 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7282 (mm-30) REVERT: E 51 ASP cc_start: 0.8795 (m-30) cc_final: 0.8313 (m-30) REVERT: E 175 GLU cc_start: 0.8039 (tt0) cc_final: 0.7682 (mt-10) REVERT: E 187 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6129 (pt0) REVERT: E 192 GLN cc_start: 0.7955 (tp40) cc_final: 0.7641 (tm-30) REVERT: G 18 ARG cc_start: 0.7251 (ttp-170) cc_final: 0.6735 (ttt-90) REVERT: G 21 ASN cc_start: 0.8094 (t0) cc_final: 0.7667 (m110) REVERT: G 25 LYS cc_start: 0.7865 (mttt) cc_final: 0.7587 (ttmm) REVERT: G 51 ASP cc_start: 0.8780 (m-30) cc_final: 0.8304 (m-30) REVERT: G 154 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7422 (mtp180) REVERT: G 175 GLU cc_start: 0.7831 (tt0) cc_final: 0.7544 (mt-10) REVERT: G 187 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6201 (pt0) REVERT: G 197 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.6190 (p0) REVERT: I 13 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: I 18 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6745 (ttt-90) REVERT: I 25 LYS cc_start: 0.7669 (mttt) cc_final: 0.7392 (ttmm) REVERT: I 51 ASP cc_start: 0.8762 (m-30) cc_final: 0.8371 (m-30) REVERT: I 68 MET cc_start: 0.8699 (mtm) cc_final: 0.8451 (mtm) REVERT: I 118 MET cc_start: 0.8575 (mtp) cc_final: 0.8340 (mtp) REVERT: I 154 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7468 (mtt90) REVERT: I 175 GLU cc_start: 0.7897 (tt0) cc_final: 0.7527 (mt-10) REVERT: K 25 LYS cc_start: 0.7692 (mttt) cc_final: 0.7411 (ttmm) REVERT: K 28 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7362 (mm-30) REVERT: K 51 ASP cc_start: 0.8816 (m-30) cc_final: 0.8396 (m-30) REVERT: K 175 GLU cc_start: 0.8045 (tt0) cc_final: 0.7684 (mt-10) REVERT: K 187 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6144 (pt0) REVERT: K 192 GLN cc_start: 0.7962 (tp40) cc_final: 0.7649 (tm-30) outliers start: 36 outliers final: 23 residues processed: 282 average time/residue: 1.8093 time to fit residues: 539.1550 Evaluate side-chains 302 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 102 SER 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 102 SER 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 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 102 SER 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 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 18 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 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 = 0.3789 r_free = 0.3789 target = 0.155429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118328 restraints weight = 10425.116| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.32 r_work: 0.3224 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3050 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= 0.133 Angle : 0.503 7.651 14364 Z= 0.253 Chirality : 0.042 0.165 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.165 19.138 1410 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.81 % Allowed : 18.57 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1308 helix: 1.78 (0.18), residues: 894 sheet: -0.65 (0.74), residues: 54 loop : 0.59 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 80 HIS 0.002 0.000 HIS A 12 PHE 0.012 0.002 PHE E 32 TYR 0.010 0.002 TYR K 145 ARG 0.007 0.000 ARG K 154 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 642) hydrogen bonds : angle 3.35234 ( 1890) covalent geometry : bond 0.00330 (10566) covalent geometry : angle 0.50331 (14364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10170.38 seconds wall clock time: 179 minutes 4.61 seconds (10744.61 seconds total)