Starting phenix.real_space_refine on Sun Dec 29 09:24:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cky_16706/12_2024/8cky_16706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cky_16706/12_2024/8cky_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_16706/12_2024/8cky_16706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cky_16706/12_2024/8cky_16706.map" model { file = "/net/cci-nas-00/data/ceres_data/8cky_16706/12_2024/8cky_16706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cky_16706/12_2024/8cky_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-5532/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: 4.54, per 1000 atoms: 0.44 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 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: 1.15 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: 2.82 Time building geometry restraints manager: 3.05 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.670 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 23.560 Find NCS groups from input model: 0.320 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.880 ------------------------------------------------------------------------------- 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= 0.270 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 *********************** 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 : 1.316 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: 1.4520 time to fit residues: 537.9219 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 : 1.126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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= 0.307 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 *********************** 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 : 1.158 Fit side-chains REVERT: A 18 ARG cc_start: 0.7263 (ttp-170) cc_final: 0.7023 (ttt-90) REVERT: A 145 TYR cc_start: 0.8174 (m-80) cc_final: 0.7905 (m-10) REVERT: A 187 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6388 (pt0) REVERT: C 51 ASP cc_start: 0.8258 (m-30) cc_final: 0.7903 (m-30) REVERT: C 66 MET cc_start: 0.8482 (mmm) cc_final: 0.8244 (mmt) REVERT: C 118 MET cc_start: 0.8733 (mtp) cc_final: 0.8406 (mtp) REVERT: C 175 GLU cc_start: 0.7268 (tt0) cc_final: 0.7024 (mt-10) REVERT: C 185 MET cc_start: 0.8091 (mtm) cc_final: 0.7727 (mtt) REVERT: C 212 GLU cc_start: 0.7105 (tt0) cc_final: 0.6694 (tt0) REVERT: E 136 LEU cc_start: 0.8566 (mp) cc_final: 0.8319 (mt) REVERT: E 175 GLU cc_start: 0.7251 (tt0) cc_final: 0.7009 (mt-10) REVERT: E 187 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6290 (pt0) REVERT: E 192 GLN cc_start: 0.7690 (tp40) cc_final: 0.7410 (tm-30) REVERT: G 18 ARG cc_start: 0.7288 (ttp-170) cc_final: 0.7035 (ttt-90) REVERT: G 145 TYR cc_start: 0.8175 (m-80) cc_final: 0.7904 (m-10) REVERT: G 187 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6389 (pt0) REVERT: I 51 ASP cc_start: 0.8260 (m-30) cc_final: 0.7900 (m-30) REVERT: I 66 MET cc_start: 0.8481 (mmm) cc_final: 0.8243 (mmt) REVERT: I 118 MET cc_start: 0.8732 (mtp) cc_final: 0.8406 (mtp) REVERT: I 175 GLU cc_start: 0.7270 (tt0) cc_final: 0.7024 (mt-10) REVERT: I 185 MET cc_start: 0.8092 (mtm) cc_final: 0.7727 (mtt) REVERT: I 212 GLU cc_start: 0.7109 (tt0) cc_final: 0.6698 (tt0) REVERT: K 136 LEU cc_start: 0.8564 (mp) cc_final: 0.8320 (mt) REVERT: K 175 GLU cc_start: 0.7255 (tt0) cc_final: 0.7011 (mt-10) REVERT: K 187 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6290 (pt0) REVERT: K 192 GLN cc_start: 0.7691 (tp40) cc_final: 0.7411 (tm-30) outliers start: 52 outliers final: 16 residues processed: 313 average time/residue: 1.5043 time to fit residues: 499.3003 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 : 1.204 ------------------------------------------------------------------------------- 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 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 99 optimal weight: 0.0870 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN 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 21 ASN 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10566 Z= 0.221 Angle : 0.501 6.492 14364 Z= 0.248 Chirality : 0.042 0.157 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.316 20.184 1410 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.80 % Allowed : 14.22 % Favored : 81.97 % 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: 1.93 (0.22), residues: 1308 helix: 1.78 (0.17), residues: 894 sheet: -0.58 (0.56), residues: 54 loop : 0.50 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 117 HIS 0.002 0.000 HIS G 84 PHE 0.012 0.002 PHE K 32 TYR 0.007 0.001 TYR G 169 ARG 0.005 0.000 ARG K 154 *********************** 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 339 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 1.288 Fit side-chains REVERT: A 145 TYR cc_start: 0.8168 (m-80) cc_final: 0.7880 (m-10) REVERT: A 148 THR cc_start: 0.8021 (m) cc_final: 0.7794 (t) REVERT: A 187 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6293 (pt0) REVERT: C 51 ASP cc_start: 0.8190 (m-30) cc_final: 0.7825 (m-30) REVERT: C 66 MET cc_start: 0.8458 (mmm) cc_final: 0.8223 (mmt) REVERT: C 118 MET cc_start: 0.8723 (mtp) cc_final: 0.8448 (mtp) REVERT: C 197 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6325 (p0) REVERT: C 212 GLU cc_start: 0.6973 (tt0) cc_final: 0.6665 (tt0) REVERT: E 136 LEU cc_start: 0.8492 (mp) cc_final: 0.8261 (mt) REVERT: E 175 GLU cc_start: 0.7286 (tt0) cc_final: 0.7054 (mt-10) REVERT: E 187 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6237 (pt0) REVERT: E 192 GLN cc_start: 0.7715 (tp40) cc_final: 0.7453 (tm-30) REVERT: E 197 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6314 (p0) REVERT: G 145 TYR cc_start: 0.8169 (m-80) cc_final: 0.7879 (m-10) REVERT: G 148 THR cc_start: 0.8028 (m) cc_final: 0.7773 (t) REVERT: G 187 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6292 (pt0) REVERT: I 51 ASP cc_start: 0.8180 (m-30) cc_final: 0.7815 (m-30) REVERT: I 66 MET cc_start: 0.8456 (mmm) cc_final: 0.8221 (mmt) REVERT: I 118 MET cc_start: 0.8724 (mtp) cc_final: 0.8448 (mtp) REVERT: I 197 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6326 (p0) REVERT: I 212 GLU cc_start: 0.6970 (tt0) cc_final: 0.6665 (tt0) REVERT: K 136 LEU cc_start: 0.8495 (mp) cc_final: 0.8265 (mt) REVERT: K 175 GLU cc_start: 0.7287 (tt0) cc_final: 0.7057 (mt-10) REVERT: K 187 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6236 (pt0) REVERT: K 192 GLN cc_start: 0.7715 (tp40) cc_final: 0.7453 (tm-30) REVERT: K 197 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6313 (p0) outliers start: 42 outliers final: 16 residues processed: 299 average time/residue: 1.5696 time to fit residues: 497.1300 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 : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 120 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 112 GLN A 219 GLN C 112 GLN C 193 ASN C 219 GLN E 112 GLN E 179 GLN G 21 ASN G 112 GLN G 219 GLN I 112 GLN I 193 ASN I 219 GLN K 112 GLN K 179 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2804 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= 0.229 Angle : 0.506 6.514 14364 Z= 0.249 Chirality : 0.042 0.163 1632 Planarity : 0.004 0.034 1854 Dihedral : 4.245 20.050 1410 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 3.89 % Allowed : 14.67 % Favored : 81.43 % 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: 2.00 (0.23), residues: 1308 helix: 1.84 (0.17), residues: 894 sheet: -0.59 (0.61), residues: 54 loop : 0.50 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 23 HIS 0.002 0.001 HIS A 12 PHE 0.011 0.002 PHE E 32 TYR 0.009 0.001 TYR E 145 ARG 0.005 0.000 ARG E 154 *********************** 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 329 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.286 Fit side-chains REVERT: A 145 TYR cc_start: 0.8170 (m-80) cc_final: 0.7942 (m-10) REVERT: A 187 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6307 (pt0) REVERT: A 197 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6318 (p0) REVERT: C 18 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6841 (ttt-90) REVERT: C 30 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7624 (mtpp) REVERT: C 51 ASP cc_start: 0.8237 (m-30) cc_final: 0.7874 (m-30) REVERT: C 66 MET cc_start: 0.8447 (mmm) cc_final: 0.8232 (mmt) REVERT: C 118 MET cc_start: 0.8744 (mtp) cc_final: 0.8467 (mtp) REVERT: C 197 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6305 (p0) REVERT: E 136 LEU cc_start: 0.8503 (mp) cc_final: 0.8272 (mt) REVERT: E 175 GLU cc_start: 0.7271 (tt0) cc_final: 0.7054 (mt-10) REVERT: E 179 GLN cc_start: 0.8510 (tp40) cc_final: 0.8200 (tp-100) REVERT: E 187 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6270 (pt0) REVERT: E 192 GLN cc_start: 0.7710 (tp40) cc_final: 0.7457 (tm-30) REVERT: G 145 TYR cc_start: 0.8171 (m-80) cc_final: 0.7942 (m-10) REVERT: G 187 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6308 (pt0) REVERT: G 197 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6317 (p0) REVERT: I 18 ARG cc_start: 0.7460 (ttm-80) cc_final: 0.6765 (ttt-90) REVERT: I 30 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7629 (mtpp) REVERT: I 51 ASP cc_start: 0.8237 (m-30) cc_final: 0.7873 (m-30) REVERT: I 66 MET cc_start: 0.8445 (mmm) cc_final: 0.8230 (mmt) REVERT: I 118 MET cc_start: 0.8744 (mtp) cc_final: 0.8468 (mtp) REVERT: I 197 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6305 (p0) REVERT: K 18 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.6702 (ttt-90) REVERT: K 136 LEU cc_start: 0.8489 (mp) cc_final: 0.8255 (mt) REVERT: K 175 GLU cc_start: 0.7274 (tt0) cc_final: 0.7056 (mt-10) REVERT: K 179 GLN cc_start: 0.8511 (tp40) cc_final: 0.8201 (tp-100) REVERT: K 187 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6272 (pt0) REVERT: K 192 GLN cc_start: 0.7711 (tp40) cc_final: 0.7458 (tm-30) outliers start: 43 outliers final: 18 residues processed: 292 average time/residue: 1.6067 time to fit residues: 496.4632 Evaluate side-chains 304 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 279 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 11 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 30 LYS 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 11 VAL 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 11 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 30 LYS 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 11 VAL 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 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 21 ASN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10566 Z= 0.295 Angle : 0.525 6.629 14364 Z= 0.261 Chirality : 0.043 0.155 1632 Planarity : 0.005 0.036 1854 Dihedral : 4.373 20.829 1410 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.08 % Allowed : 16.12 % Favored : 79.80 % 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: 1.90 (0.23), residues: 1308 helix: 1.72 (0.17), residues: 894 sheet: -0.40 (0.65), residues: 54 loop : 0.55 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 80 HIS 0.003 0.001 HIS G 12 PHE 0.013 0.002 PHE E 32 TYR 0.011 0.002 TYR E 145 ARG 0.006 0.000 ARG E 154 *********************** 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 324 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 1.261 Fit side-chains REVERT: A 145 TYR cc_start: 0.8196 (m-80) cc_final: 0.7956 (m-10) REVERT: A 187 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6335 (pt0) REVERT: A 197 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6840 (p0) REVERT: C 18 ARG cc_start: 0.7404 (mtm-85) cc_final: 0.6837 (ttt-90) REVERT: C 51 ASP cc_start: 0.8266 (m-30) cc_final: 0.7897 (m-30) REVERT: C 118 MET cc_start: 0.8719 (mtp) cc_final: 0.8424 (mtp) REVERT: C 197 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6343 (p0) REVERT: C 215 MET cc_start: 0.7806 (mtp) cc_final: 0.7536 (mtp) REVERT: E 51 ASP cc_start: 0.8268 (m-30) cc_final: 0.7953 (m-30) REVERT: E 79 GLU cc_start: 0.7408 (tp30) cc_final: 0.7186 (tp30) REVERT: E 175 GLU cc_start: 0.7372 (tt0) cc_final: 0.7125 (mt-10) REVERT: E 187 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6286 (pt0) REVERT: E 192 GLN cc_start: 0.7737 (tp40) cc_final: 0.7489 (tm-30) REVERT: E 197 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6560 (p0) REVERT: G 145 TYR cc_start: 0.8195 (m-80) cc_final: 0.7955 (m-10) REVERT: G 187 GLU cc_start: 0.6652 (mt-10) cc_final: 0.6335 (pt0) REVERT: G 197 ASP cc_start: 0.7112 (OUTLIER) cc_final: 0.6838 (p0) REVERT: I 18 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6698 (ttt-90) REVERT: I 51 ASP cc_start: 0.8265 (m-30) cc_final: 0.7897 (m-30) REVERT: I 118 MET cc_start: 0.8719 (mtp) cc_final: 0.8425 (mtp) REVERT: I 197 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6344 (p0) REVERT: I 215 MET cc_start: 0.7806 (mtp) cc_final: 0.7537 (mtp) REVERT: K 18 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.6683 (ttt-90) REVERT: K 51 ASP cc_start: 0.8268 (m-30) cc_final: 0.7946 (m-30) REVERT: K 79 GLU cc_start: 0.7409 (tp30) cc_final: 0.7188 (tp30) REVERT: K 175 GLU cc_start: 0.7374 (tt0) cc_final: 0.7128 (mt-10) REVERT: K 187 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6245 (pt0) REVERT: K 192 GLN cc_start: 0.7731 (tp40) cc_final: 0.7488 (tm-30) REVERT: K 197 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6559 (p0) outliers start: 45 outliers final: 19 residues processed: 289 average time/residue: 1.5708 time to fit residues: 480.8207 Evaluate side-chains 296 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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 11 VAL 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 E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 18 ARG 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 11 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 21 ASN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10566 Z= 0.278 Angle : 0.522 6.881 14364 Z= 0.258 Chirality : 0.043 0.173 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.333 20.411 1410 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 4.80 % Allowed : 15.76 % Favored : 79.44 % 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: 1.86 (0.23), residues: 1308 helix: 1.68 (0.17), residues: 894 sheet: -0.27 (0.68), residues: 54 loop : 0.56 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 23 HIS 0.002 0.001 HIS I 84 PHE 0.013 0.002 PHE E 32 TYR 0.012 0.002 TYR E 145 ARG 0.006 0.000 ARG E 154 *********************** 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 334 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 1.260 Fit side-chains REVERT: A 55 MET cc_start: 0.8285 (mtp) cc_final: 0.7953 (mtp) REVERT: A 145 TYR cc_start: 0.8181 (m-80) cc_final: 0.7940 (m-10) REVERT: A 187 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6311 (pt0) REVERT: A 197 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6365 (p0) REVERT: C 18 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6789 (ttt-90) REVERT: C 51 ASP cc_start: 0.8268 (m-30) cc_final: 0.7900 (m-30) REVERT: C 68 MET cc_start: 0.8533 (mtm) cc_final: 0.8264 (mtm) REVERT: C 118 MET cc_start: 0.8724 (mtp) cc_final: 0.8462 (mtp) REVERT: C 197 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6365 (p0) REVERT: E 18 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.6810 (ttt-90) REVERT: E 51 ASP cc_start: 0.8272 (m-30) cc_final: 0.7914 (m-30) REVERT: E 175 GLU cc_start: 0.7348 (tt0) cc_final: 0.7119 (mt-10) REVERT: E 187 GLU cc_start: 0.6530 (mt-10) cc_final: 0.6282 (pt0) REVERT: E 192 GLN cc_start: 0.7743 (tp40) cc_final: 0.7495 (tm-30) REVERT: G 55 MET cc_start: 0.8284 (mtp) cc_final: 0.7953 (mtp) REVERT: G 145 TYR cc_start: 0.8181 (m-80) cc_final: 0.7939 (m-10) REVERT: G 187 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6313 (pt0) REVERT: G 197 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6359 (p0) REVERT: I 18 ARG cc_start: 0.7390 (ttm-80) cc_final: 0.6704 (ttt-90) REVERT: I 51 ASP cc_start: 0.8268 (m-30) cc_final: 0.7898 (m-30) REVERT: I 68 MET cc_start: 0.8527 (mtm) cc_final: 0.8265 (mtm) REVERT: I 118 MET cc_start: 0.8724 (mtp) cc_final: 0.8462 (mtp) REVERT: I 197 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6364 (p0) REVERT: K 18 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6675 (ttt-90) REVERT: K 51 ASP cc_start: 0.8284 (m-30) cc_final: 0.7919 (m-30) REVERT: K 175 GLU cc_start: 0.7351 (tt0) cc_final: 0.7125 (mt-10) REVERT: K 187 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6263 (pt0) REVERT: K 192 GLN cc_start: 0.7734 (tp40) cc_final: 0.7495 (tm-30) outliers start: 53 outliers final: 30 residues processed: 290 average time/residue: 1.5241 time to fit residues: 468.0258 Evaluate side-chains 306 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 148 THR 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 18 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 148 THR 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 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 I residue 203 LYS Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 96 MET Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 203 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 21 ASN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2940 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= 0.255 Angle : 0.520 7.623 14364 Z= 0.257 Chirality : 0.043 0.184 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.284 20.063 1410 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.08 % Allowed : 16.85 % Favored : 79.08 % 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: 1.86 (0.23), residues: 1308 helix: 1.71 (0.17), residues: 894 sheet: -0.71 (0.66), residues: 54 loop : 0.55 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS K 12 PHE 0.012 0.002 PHE K 32 TYR 0.012 0.002 TYR K 145 ARG 0.006 0.000 ARG C 154 *********************** 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 329 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.329 Fit side-chains REVERT: A 145 TYR cc_start: 0.8175 (m-80) cc_final: 0.7913 (m-10) REVERT: A 185 MET cc_start: 0.8074 (mtm) cc_final: 0.7812 (mtt) REVERT: A 187 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6316 (pt0) REVERT: A 197 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6391 (p0) REVERT: C 18 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6789 (ttt-90) REVERT: C 51 ASP cc_start: 0.8248 (m-30) cc_final: 0.7868 (m-30) REVERT: C 68 MET cc_start: 0.8511 (mtm) cc_final: 0.8236 (mtm) REVERT: C 118 MET cc_start: 0.8723 (mtp) cc_final: 0.8470 (mtp) REVERT: C 197 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6363 (p0) REVERT: E 18 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.6837 (ttt-90) REVERT: E 51 ASP cc_start: 0.8260 (m-30) cc_final: 0.7855 (m-30) REVERT: E 136 LEU cc_start: 0.8524 (mp) cc_final: 0.8319 (mt) REVERT: E 175 GLU cc_start: 0.7312 (tt0) cc_final: 0.7096 (mt-10) REVERT: E 187 GLU cc_start: 0.6526 (mt-10) cc_final: 0.6286 (pt0) REVERT: E 192 GLN cc_start: 0.7710 (tp40) cc_final: 0.7465 (tm-30) REVERT: E 197 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6567 (p0) REVERT: G 145 TYR cc_start: 0.8175 (m-80) cc_final: 0.7913 (m-10) REVERT: G 185 MET cc_start: 0.8078 (mtm) cc_final: 0.7818 (mtt) REVERT: G 187 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6316 (pt0) REVERT: G 197 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6390 (p0) REVERT: I 18 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6763 (ttt-90) REVERT: I 51 ASP cc_start: 0.8246 (m-30) cc_final: 0.7867 (m-30) REVERT: I 68 MET cc_start: 0.8509 (mtm) cc_final: 0.8232 (mtm) REVERT: I 118 MET cc_start: 0.8723 (mtp) cc_final: 0.8470 (mtp) REVERT: I 197 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6361 (p0) REVERT: K 18 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6670 (ttt-90) REVERT: K 51 ASP cc_start: 0.8278 (m-30) cc_final: 0.7889 (m-30) REVERT: K 175 GLU cc_start: 0.7314 (tt0) cc_final: 0.7104 (mt-10) REVERT: K 187 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6257 (pt0) REVERT: K 192 GLN cc_start: 0.7685 (tp40) cc_final: 0.7451 (tm-30) REVERT: K 197 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6513 (p0) outliers start: 45 outliers final: 26 residues processed: 293 average time/residue: 1.5099 time to fit residues: 468.8414 Evaluate side-chains 303 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 148 THR 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 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 E residue 197 ASP Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 148 THR 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 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 102 SER Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 197 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 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 21 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN G 21 ASN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2965 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= 0.266 Angle : 0.535 7.381 14364 Z= 0.264 Chirality : 0.043 0.171 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.304 20.165 1410 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.53 % Allowed : 17.12 % Favored : 78.35 % 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: 1.70 (0.17), residues: 894 sheet: -0.89 (0.70), residues: 54 loop : 0.56 (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 G 12 PHE 0.012 0.002 PHE K 32 TYR 0.013 0.002 TYR K 145 ARG 0.007 0.000 ARG I 154 *********************** 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 332 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 1.231 Fit side-chains REVERT: A 55 MET cc_start: 0.8252 (mtp) cc_final: 0.7860 (mtp) REVERT: A 145 TYR cc_start: 0.8170 (m-80) cc_final: 0.7908 (m-10) REVERT: A 185 MET cc_start: 0.8088 (mtm) cc_final: 0.7879 (mtt) REVERT: A 187 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6282 (pt0) REVERT: A 197 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6372 (p0) REVERT: C 18 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6797 (ttt-90) REVERT: C 51 ASP cc_start: 0.8246 (m-30) cc_final: 0.7866 (m-30) REVERT: C 118 MET cc_start: 0.8717 (mtp) cc_final: 0.8464 (mtp) REVERT: C 197 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6370 (p0) REVERT: E 18 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.6835 (ttt-90) REVERT: E 51 ASP cc_start: 0.8278 (m-30) cc_final: 0.7893 (m-30) REVERT: E 140 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8088 (mtpm) REVERT: E 175 GLU cc_start: 0.7317 (tt0) cc_final: 0.7102 (mt-10) REVERT: E 187 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6279 (pt0) REVERT: E 192 GLN cc_start: 0.7712 (tp40) cc_final: 0.7468 (tm-30) REVERT: G 55 MET cc_start: 0.8239 (mtp) cc_final: 0.7863 (mtp) REVERT: G 145 TYR cc_start: 0.8171 (m-80) cc_final: 0.7907 (m-10) REVERT: G 187 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6282 (pt0) REVERT: G 197 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6373 (p0) REVERT: I 13 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: I 18 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.6761 (ttt-90) REVERT: I 51 ASP cc_start: 0.8246 (m-30) cc_final: 0.7865 (m-30) REVERT: I 118 MET cc_start: 0.8718 (mtp) cc_final: 0.8464 (mtp) REVERT: I 197 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6366 (p0) REVERT: K 18 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.6827 (ttt-90) REVERT: K 51 ASP cc_start: 0.8273 (m-30) cc_final: 0.7841 (m-30) REVERT: K 140 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8094 (mtpm) REVERT: K 175 GLU cc_start: 0.7312 (tt0) cc_final: 0.7097 (mt-10) REVERT: K 187 GLU cc_start: 0.6525 (mt-10) cc_final: 0.6224 (pt0) REVERT: K 192 GLN cc_start: 0.7681 (tp40) cc_final: 0.7445 (tm-30) outliers start: 50 outliers final: 31 residues processed: 292 average time/residue: 1.6339 time to fit residues: 508.6645 Evaluate side-chains 313 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 LYS 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 102 SER 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 102 SER Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 203 LYS 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 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 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 102 SER Chi-restraints excluded: chain K residue 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 76 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 21 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN E 179 GLN G 21 ASN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10566 Z= 0.268 Angle : 0.546 8.147 14364 Z= 0.268 Chirality : 0.044 0.174 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.302 20.127 1410 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.62 % Allowed : 17.48 % Favored : 77.90 % 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: 1.83 (0.23), residues: 1308 helix: 1.68 (0.17), residues: 894 sheet: -0.70 (0.72), residues: 54 loop : 0.56 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 80 HIS 0.003 0.001 HIS G 12 PHE 0.013 0.002 PHE K 32 TYR 0.013 0.002 TYR K 145 ARG 0.007 0.000 ARG C 154 *********************** 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 329 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 1.166 Fit side-chains REVERT: A 55 MET cc_start: 0.8260 (mtp) cc_final: 0.7877 (mtp) REVERT: A 145 TYR cc_start: 0.8174 (m-80) cc_final: 0.7909 (m-10) REVERT: A 187 GLU cc_start: 0.6570 (mt-10) cc_final: 0.6289 (pt0) REVERT: A 197 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6421 (p0) REVERT: C 13 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: C 18 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6800 (ttt-90) REVERT: C 51 ASP cc_start: 0.8245 (m-30) cc_final: 0.7864 (m-30) REVERT: C 68 MET cc_start: 0.8530 (mtm) cc_final: 0.8238 (mtm) REVERT: C 118 MET cc_start: 0.8721 (mtp) cc_final: 0.8473 (mtp) REVERT: E 18 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.6827 (ttt-90) REVERT: E 51 ASP cc_start: 0.8281 (m-30) cc_final: 0.7886 (m-30) REVERT: E 140 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8088 (mtpm) REVERT: E 175 GLU cc_start: 0.7368 (tt0) cc_final: 0.7130 (mt-10) REVERT: E 179 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8396 (tp40) REVERT: E 187 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6274 (pt0) REVERT: E 192 GLN cc_start: 0.7724 (tp40) cc_final: 0.7451 (tm-30) REVERT: G 55 MET cc_start: 0.8266 (mtp) cc_final: 0.7877 (mtp) REVERT: G 145 TYR cc_start: 0.8176 (m-80) cc_final: 0.7907 (m-10) REVERT: G 187 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6272 (pt0) REVERT: G 197 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6420 (p0) REVERT: I 13 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: I 18 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.6768 (ttt-90) REVERT: I 51 ASP cc_start: 0.8246 (m-30) cc_final: 0.7866 (m-30) REVERT: I 68 MET cc_start: 0.8528 (mtm) cc_final: 0.8237 (mtm) REVERT: I 118 MET cc_start: 0.8722 (mtp) cc_final: 0.8474 (mtp) REVERT: K 18 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.6824 (ttt-90) REVERT: K 51 ASP cc_start: 0.8278 (m-30) cc_final: 0.7837 (m-30) REVERT: K 136 LEU cc_start: 0.8531 (mp) cc_final: 0.8330 (mt) REVERT: K 140 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8092 (mtpm) REVERT: K 175 GLU cc_start: 0.7312 (tt0) cc_final: 0.7097 (mt-10) REVERT: K 187 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6225 (pt0) REVERT: K 192 GLN cc_start: 0.7716 (tp40) cc_final: 0.7445 (tm-30) outliers start: 51 outliers final: 33 residues processed: 289 average time/residue: 1.5763 time to fit residues: 482.3721 Evaluate side-chains 314 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 LYS 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 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 203 LYS 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 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 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 219 GLN C 112 GLN C 193 ASN C 219 GLN E 112 GLN E 179 GLN G 21 ASN G 219 GLN I 112 GLN I 193 ASN I 219 GLN K 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3013 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= 0.257 Angle : 0.541 7.682 14364 Z= 0.268 Chirality : 0.044 0.174 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.280 19.918 1410 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.80 % Allowed : 18.66 % Favored : 77.54 % 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: 1.83 (0.23), residues: 1308 helix: 1.67 (0.17), residues: 894 sheet: -0.75 (0.73), residues: 54 loop : 0.58 (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 A 12 PHE 0.012 0.002 PHE K 32 TYR 0.012 0.002 TYR E 145 ARG 0.007 0.000 ARG E 154 ********************** 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 316 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 1.235 Fit side-chains REVERT: A 55 MET cc_start: 0.8273 (mtp) cc_final: 0.7870 (mtp) REVERT: A 145 TYR cc_start: 0.8157 (m-80) cc_final: 0.7888 (m-10) REVERT: A 187 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6273 (pt0) REVERT: A 197 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6406 (p0) REVERT: C 13 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: C 18 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6800 (ttt-90) REVERT: C 51 ASP cc_start: 0.8241 (m-30) cc_final: 0.7861 (m-30) REVERT: C 68 MET cc_start: 0.8544 (mtm) cc_final: 0.8249 (mtm) REVERT: C 118 MET cc_start: 0.8723 (mtp) cc_final: 0.8477 (mtp) REVERT: E 18 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.6842 (ttt-90) REVERT: E 51 ASP cc_start: 0.8283 (m-30) cc_final: 0.7851 (m-30) REVERT: E 140 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8085 (mtpm) REVERT: E 175 GLU cc_start: 0.7385 (tt0) cc_final: 0.7146 (mt-10) REVERT: E 179 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8431 (tp40) REVERT: E 187 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6248 (pt0) REVERT: E 192 GLN cc_start: 0.7720 (tp40) cc_final: 0.7450 (tm-30) REVERT: G 55 MET cc_start: 0.8262 (mtp) cc_final: 0.7882 (mtp) REVERT: G 145 TYR cc_start: 0.8160 (m-80) cc_final: 0.7890 (m-10) REVERT: G 187 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6217 (pt0) REVERT: G 197 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6408 (p0) REVERT: I 13 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: I 18 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.6764 (ttt-90) REVERT: I 51 ASP cc_start: 0.8242 (m-30) cc_final: 0.7860 (m-30) REVERT: I 68 MET cc_start: 0.8544 (mtm) cc_final: 0.8249 (mtm) REVERT: I 118 MET cc_start: 0.8722 (mtp) cc_final: 0.8476 (mtp) REVERT: K 18 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6831 (ttt-90) REVERT: K 51 ASP cc_start: 0.8258 (m-30) cc_final: 0.7814 (m-30) REVERT: K 140 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8090 (mtpm) REVERT: K 175 GLU cc_start: 0.7308 (tt0) cc_final: 0.7098 (mt-10) REVERT: K 187 GLU cc_start: 0.6531 (mt-10) cc_final: 0.6219 (pt0) REVERT: K 192 GLN cc_start: 0.7712 (tp40) cc_final: 0.7444 (tm-30) outliers start: 42 outliers final: 30 residues processed: 285 average time/residue: 1.5455 time to fit residues: 466.3474 Evaluate side-chains 307 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 LYS 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 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 140 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 203 LYS 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 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 140 LYS Chi-restraints excluded: chain K residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 219 GLN C 112 GLN C 219 GLN E 112 GLN E 179 GLN G 21 ASN G 219 GLN I 112 GLN I 219 GLN K 112 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115954 restraints weight = 10345.320| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.32 r_work: 0.3215 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3067 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= 0.216 Angle : 0.526 7.705 14364 Z= 0.261 Chirality : 0.042 0.168 1632 Planarity : 0.004 0.035 1854 Dihedral : 4.208 19.310 1410 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.89 % Allowed : 19.11 % Favored : 76.99 % 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: 1.91 (0.23), residues: 1308 helix: 1.74 (0.18), residues: 894 sheet: -0.84 (0.73), 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 K 32 TYR 0.011 0.001 TYR K 145 ARG 0.007 0.000 ARG C 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6532.75 seconds wall clock time: 117 minutes 13.88 seconds (7033.88 seconds total)