Starting phenix.real_space_refine on Tue Mar 3 13:43:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a03_15046/03_2026/8a03_15046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a03_15046/03_2026/8a03_15046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2026/8a03_15046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2026/8a03_15046.map" model { file = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2026/8a03_15046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2026/8a03_15046.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 15 5.16 5 C 3495 2.51 5 N 885 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 1 Chain: "L" Number of atoms: 1837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1837 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Restraints were copied for chains: K, J Time building chain proxies: 1.24, per 1000 atoms: 0.23 Number of scatterers: 5511 At special positions: 0 Unit cell: (96.72, 101.68, 57.04, 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 15 16.00 O 1116 8.00 N 885 7.00 C 3495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 406.6 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 10.5% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'L' and resid 60 through 66 Processing helix chain 'L' and resid 178 through 190 removed outlier: 3.686A pdb=" N ILE L 189 " --> pdb=" O LEU L 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 178 through 190 removed outlier: 3.687A pdb=" N ILE K 189 " --> pdb=" O LEU K 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'J' and resid 60 through 66 Processing helix chain 'J' and resid 178 through 190 removed outlier: 3.686A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS L 2 " --> pdb=" O GLY L 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY L 119 " --> pdb=" O LYS L 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 4 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 15 through 17 removed outlier: 7.221A pdb=" N ILE L 40 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN L 56 " --> pdb=" O ILE L 40 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE L 42 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 93 through 94 removed outlier: 5.139A pdb=" N SER L 93 " --> pdb=" O THR L 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN L 230 " --> pdb=" O THR L 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG L 234 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU L 153 " --> pdb=" O ARG L 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 143 through 147 removed outlier: 6.679A pdb=" N GLN L 168 " --> pdb=" O VAL L 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE L 219 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER L 166 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE L 221 " --> pdb=" O ASP L 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP L 164 " --> pdb=" O ILE L 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS L 223 " --> pdb=" O VAL L 162 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL L 162 " --> pdb=" O LYS L 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL L 175 " --> pdb=" O TYR L 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'K' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS K 2 " --> pdb=" O GLY K 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY K 119 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 4 " --> pdb=" O LEU K 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 15 through 17 removed outlier: 7.220A pdb=" N ILE K 40 " --> pdb=" O ASN K 56 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN K 56 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 42 " --> pdb=" O LEU K 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 93 through 94 removed outlier: 5.137A pdb=" N SER K 93 " --> pdb=" O THR K 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN K 230 " --> pdb=" O THR K 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 234 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU K 153 " --> pdb=" O ARG K 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 143 through 147 removed outlier: 6.679A pdb=" N GLN K 168 " --> pdb=" O VAL K 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE K 219 " --> pdb=" O SER K 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER K 166 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE K 221 " --> pdb=" O ASP K 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP K 164 " --> pdb=" O ILE K 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS K 223 " --> pdb=" O VAL K 162 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL K 162 " --> pdb=" O LYS K 223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL K 175 " --> pdb=" O TYR K 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 194 through 195 Processing sheet with id=AB4, first strand: chain 'J' and resid 2 through 7 removed outlier: 5.738A pdb=" N LYS J 2 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY J 119 " --> pdb=" O LYS J 2 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 4 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 15 through 17 removed outlier: 7.220A pdb=" N ILE J 40 " --> pdb=" O ASN J 56 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN J 56 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE J 42 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 93 through 94 removed outlier: 5.138A pdb=" N SER J 93 " --> pdb=" O THR J 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'J' and resid 128 through 137 removed outlier: 5.323A pdb=" N ASN J 230 " --> pdb=" O THR J 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG J 234 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU J 153 " --> pdb=" O ARG J 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 143 through 147 removed outlier: 6.678A pdb=" N GLN J 168 " --> pdb=" O VAL J 217 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE J 219 " --> pdb=" O SER J 166 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER J 166 " --> pdb=" O ILE J 219 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE J 221 " --> pdb=" O ASP J 164 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP J 164 " --> pdb=" O ILE J 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS J 223 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL J 162 " --> pdb=" O LYS J 223 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL J 175 " --> pdb=" O TYR J 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 194 through 195 210 hydrogen bonds defined for protein. 540 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: 0.68 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1818 1.34 - 1.46: 1003 1.46 - 1.57: 2726 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5571 Sorted by residual: bond pdb=" C VAL K 148 " pdb=" O VAL K 148 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 7.90e-01 bond pdb=" C VAL L 148 " pdb=" O VAL L 148 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.73e-01 bond pdb=" C VAL J 148 " pdb=" O VAL J 148 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.54e-01 bond pdb=" CG LEU K 117 " pdb=" CD2 LEU K 117 " ideal model delta sigma weight residual 1.521 1.503 0.018 3.30e-02 9.18e+02 2.81e-01 bond pdb=" CG LEU J 117 " pdb=" CD2 LEU J 117 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.80e-01 ... (remaining 5566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 7232 0.91 - 1.81: 242 1.81 - 2.72: 48 2.72 - 3.63: 23 3.63 - 4.53: 3 Bond angle restraints: 7548 Sorted by residual: angle pdb=" C LEU L 26 " pdb=" N SER L 27 " pdb=" CA SER L 27 " ideal model delta sigma weight residual 122.73 120.05 2.68 1.62e+00 3.81e-01 2.73e+00 angle pdb=" C LEU J 26 " pdb=" N SER J 27 " pdb=" CA SER J 27 " ideal model delta sigma weight residual 122.73 120.08 2.65 1.62e+00 3.81e-01 2.69e+00 angle pdb=" C LEU K 26 " pdb=" N SER K 27 " pdb=" CA SER K 27 " ideal model delta sigma weight residual 122.73 120.11 2.62 1.62e+00 3.81e-01 2.61e+00 angle pdb=" CA LEU K 26 " pdb=" CB LEU K 26 " pdb=" CG LEU K 26 " ideal model delta sigma weight residual 116.30 120.83 -4.53 3.50e+00 8.16e-02 1.68e+00 angle pdb=" CA LEU L 26 " pdb=" CB LEU L 26 " pdb=" CG LEU L 26 " ideal model delta sigma weight residual 116.30 120.81 -4.51 3.50e+00 8.16e-02 1.66e+00 ... (remaining 7543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3108 17.97 - 35.94: 246 35.94 - 53.91: 45 53.91 - 71.87: 18 71.87 - 89.84: 3 Dihedral angle restraints: 3420 sinusoidal: 1329 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLN J 75 " pdb=" CB GLN J 75 " pdb=" CG GLN J 75 " pdb=" CD GLN J 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.76 46.76 3 1.50e+01 4.44e-03 8.39e+00 dihedral pdb=" CA GLN L 75 " pdb=" CB GLN L 75 " pdb=" CG GLN L 75 " pdb=" CD GLN L 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.73 46.73 3 1.50e+01 4.44e-03 8.38e+00 dihedral pdb=" CA GLN K 75 " pdb=" CB GLN K 75 " pdb=" CG GLN K 75 " pdb=" CD GLN K 75 " ideal model delta sinusoidal sigma weight residual -60.00 -106.68 46.68 3 1.50e+01 4.44e-03 8.37e+00 ... (remaining 3417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 593 0.027 - 0.054: 173 0.054 - 0.081: 59 0.081 - 0.108: 76 0.108 - 0.135: 35 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE K 42 " pdb=" N ILE K 42 " pdb=" C ILE K 42 " pdb=" CB ILE K 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE J 42 " pdb=" N ILE J 42 " pdb=" C ILE J 42 " pdb=" CB ILE J 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE L 42 " pdb=" N ILE L 42 " pdb=" C ILE L 42 " pdb=" CB ILE L 42 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 933 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU J 178 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO J 179 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO J 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 179 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 178 " 0.014 5.00e-02 4.00e+02 2.18e-02 7.62e-01 pdb=" N PRO K 179 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO K 179 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 179 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 178 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.60e-01 pdb=" N PRO L 179 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO L 179 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO L 179 " -0.012 5.00e-02 4.00e+02 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2046 2.90 - 3.40: 4445 3.40 - 3.90: 8664 3.90 - 4.40: 9263 4.40 - 4.90: 17482 Nonbonded interactions: 41900 Sorted by model distance: nonbonded pdb=" N GLY J 22 " pdb=" O ILE J 120 " model vdw 2.399 3.120 nonbonded pdb=" N GLY L 22 " pdb=" O ILE L 120 " model vdw 2.399 3.120 nonbonded pdb=" N GLY K 22 " pdb=" O ILE K 120 " model vdw 2.399 3.120 nonbonded pdb=" N ASP J 207 " pdb=" OD1 ASP J 207 " model vdw 2.421 3.120 nonbonded pdb=" N ASP L 207 " pdb=" OD1 ASP L 207 " model vdw 2.422 3.120 ... (remaining 41895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'K' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.002 0.018 5571 Z= 0.081 Angle : 0.437 4.533 7548 Z= 0.231 Chirality : 0.044 0.135 936 Planarity : 0.002 0.022 960 Dihedral : 14.179 89.842 2064 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.33), residues: 711 helix: 1.61 (0.71), residues: 66 sheet: 1.39 (0.31), residues: 315 loop : -0.85 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 46 TYR 0.005 0.001 TYR L 43 PHE 0.004 0.001 PHE L 231 HIS 0.000 0.000 HIS K 118 Details of bonding type rmsd covalent geometry : bond 0.00168 ( 5571) covalent geometry : angle 0.43737 ( 7548) hydrogen bonds : bond 0.11095 ( 210) hydrogen bonds : angle 4.96563 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.207 Fit side-chains REVERT: L 38 GLU cc_start: 0.8123 (mp0) cc_final: 0.7697 (mp0) REVERT: L 122 GLU cc_start: 0.7407 (pt0) cc_final: 0.7192 (pt0) REVERT: L 152 ASP cc_start: 0.7491 (p0) cc_final: 0.7201 (p0) REVERT: K 100 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7666 (mt-10) REVERT: J 101 SER cc_start: 0.8415 (m) cc_final: 0.8003 (p) REVERT: J 152 ASP cc_start: 0.7273 (p0) cc_final: 0.7040 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0668 time to fit residues: 10.5298 Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN K 225 GLN J 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100047 restraints weight = 7753.578| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.05 r_work: 0.2981 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5571 Z= 0.162 Angle : 0.527 5.152 7548 Z= 0.281 Chirality : 0.048 0.146 936 Planarity : 0.003 0.031 960 Dihedral : 3.745 10.830 750 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.90 % Allowed : 6.67 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.33), residues: 711 helix: 0.59 (0.64), residues: 72 sheet: 1.37 (0.32), residues: 312 loop : -1.00 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 46 TYR 0.019 0.002 TYR L 43 PHE 0.008 0.001 PHE J 142 HIS 0.002 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5571) covalent geometry : angle 0.52734 ( 7548) hydrogen bonds : bond 0.03755 ( 210) hydrogen bonds : angle 4.72901 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.248 Fit side-chains REVERT: L 225 GLN cc_start: 0.8237 (mt0) cc_final: 0.7976 (mt0) REVERT: J 101 SER cc_start: 0.8599 (m) cc_final: 0.8197 (p) outliers start: 12 outliers final: 11 residues processed: 77 average time/residue: 0.0547 time to fit residues: 6.1252 Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 55 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 57 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 134 GLN J 16 GLN J 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102169 restraints weight = 7673.996| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.03 r_work: 0.3009 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5571 Z= 0.089 Angle : 0.439 4.075 7548 Z= 0.237 Chirality : 0.046 0.131 936 Planarity : 0.003 0.024 960 Dihedral : 3.449 11.003 750 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.59 % Allowed : 9.52 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.33), residues: 711 helix: 0.85 (0.66), residues: 72 sheet: 1.43 (0.32), residues: 306 loop : -0.99 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 46 TYR 0.014 0.001 TYR L 43 PHE 0.005 0.001 PHE J 231 HIS 0.001 0.000 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5571) covalent geometry : angle 0.43949 ( 7548) hydrogen bonds : bond 0.03080 ( 210) hydrogen bonds : angle 4.58737 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.197 Fit side-chains REVERT: L 146 ILE cc_start: 0.8431 (pt) cc_final: 0.7988 (mt) REVERT: L 225 GLN cc_start: 0.8106 (mt0) cc_final: 0.7874 (mt0) REVERT: K 122 GLU cc_start: 0.7895 (pt0) cc_final: 0.7691 (pt0) REVERT: J 101 SER cc_start: 0.8630 (m) cc_final: 0.8140 (p) REVERT: J 107 GLU cc_start: 0.8364 (tp30) cc_final: 0.8126 (tp30) REVERT: J 140 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8453 (mp0) REVERT: J 163 SER cc_start: 0.8926 (t) cc_final: 0.8602 (p) outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 0.0453 time to fit residues: 5.9032 Evaluate side-chains 88 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 168 GLN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN K 75 GLN J 16 GLN J 75 GLN J 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.094853 restraints weight = 7853.580| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.98 r_work: 0.2954 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5571 Z= 0.224 Angle : 0.576 4.598 7548 Z= 0.306 Chirality : 0.049 0.152 936 Planarity : 0.003 0.037 960 Dihedral : 4.155 12.975 750 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.38 % Allowed : 12.22 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.32), residues: 711 helix: 0.11 (0.62), residues: 72 sheet: 1.23 (0.32), residues: 306 loop : -1.26 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 46 TYR 0.018 0.002 TYR L 43 PHE 0.009 0.001 PHE K 142 HIS 0.003 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 5571) covalent geometry : angle 0.57572 ( 7548) hydrogen bonds : bond 0.04428 ( 210) hydrogen bonds : angle 4.86699 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.230 Fit side-chains REVERT: L 146 ILE cc_start: 0.8468 (pt) cc_final: 0.8139 (mt) REVERT: L 168 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: K 220 GLU cc_start: 0.8933 (tt0) cc_final: 0.8603 (tt0) REVERT: J 38 GLU cc_start: 0.8720 (mp0) cc_final: 0.8418 (mp0) REVERT: J 101 SER cc_start: 0.8696 (m) cc_final: 0.8319 (p) REVERT: J 107 GLU cc_start: 0.8463 (tp30) cc_final: 0.8259 (tp30) REVERT: J 140 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8442 (mp0) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.0526 time to fit residues: 5.3978 Evaluate side-chains 70 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101437 restraints weight = 7828.726| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.95 r_work: 0.2977 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5571 Z= 0.125 Angle : 0.478 3.830 7548 Z= 0.259 Chirality : 0.047 0.137 936 Planarity : 0.003 0.030 960 Dihedral : 3.879 13.231 750 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.22 % Allowed : 12.38 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.32), residues: 711 helix: 0.41 (0.64), residues: 72 sheet: 1.24 (0.32), residues: 306 loop : -1.24 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 46 TYR 0.007 0.001 TYR L 115 PHE 0.005 0.001 PHE K 142 HIS 0.002 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5571) covalent geometry : angle 0.47816 ( 7548) hydrogen bonds : bond 0.03585 ( 210) hydrogen bonds : angle 4.73122 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.203 Fit side-chains REVERT: L 165 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8410 (tt) REVERT: J 101 SER cc_start: 0.8664 (m) cc_final: 0.8321 (p) REVERT: J 107 GLU cc_start: 0.8446 (tp30) cc_final: 0.8232 (tp30) REVERT: J 140 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8464 (mp0) REVERT: J 149 GLN cc_start: 0.8190 (tt0) cc_final: 0.7954 (tt0) outliers start: 14 outliers final: 12 residues processed: 79 average time/residue: 0.0549 time to fit residues: 6.3985 Evaluate side-chains 78 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.0050 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 overall best weight: 2.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102171 restraints weight = 7702.641| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.90 r_work: 0.2954 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5571 Z= 0.131 Angle : 0.475 3.701 7548 Z= 0.257 Chirality : 0.046 0.137 936 Planarity : 0.003 0.027 960 Dihedral : 3.826 13.014 750 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 13.33 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.32), residues: 711 helix: 0.41 (0.64), residues: 72 sheet: 1.21 (0.32), residues: 306 loop : -1.24 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 46 TYR 0.018 0.001 TYR L 43 PHE 0.005 0.001 PHE K 142 HIS 0.002 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5571) covalent geometry : angle 0.47523 ( 7548) hydrogen bonds : bond 0.03537 ( 210) hydrogen bonds : angle 4.67269 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.183 Fit side-chains REVERT: L 101 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8378 (p) REVERT: L 165 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8332 (tt) REVERT: K 220 GLU cc_start: 0.8876 (tt0) cc_final: 0.8555 (tt0) REVERT: J 101 SER cc_start: 0.8666 (m) cc_final: 0.8279 (p) REVERT: J 107 GLU cc_start: 0.8425 (tp30) cc_final: 0.8197 (tp30) REVERT: J 149 GLN cc_start: 0.8174 (tt0) cc_final: 0.7940 (tt0) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 0.0501 time to fit residues: 5.1349 Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN K 75 GLN J 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097626 restraints weight = 7897.070| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.01 r_work: 0.2903 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5571 Z= 0.234 Angle : 0.574 5.734 7548 Z= 0.306 Chirality : 0.049 0.145 936 Planarity : 0.003 0.034 960 Dihedral : 4.238 13.961 750 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 711 helix: 0.00 (0.62), residues: 72 sheet: 1.06 (0.32), residues: 306 loop : -1.41 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 46 TYR 0.018 0.002 TYR L 43 PHE 0.007 0.001 PHE K 142 HIS 0.003 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 5571) covalent geometry : angle 0.57363 ( 7548) hydrogen bonds : bond 0.04414 ( 210) hydrogen bonds : angle 4.84712 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.221 Fit side-chains REVERT: L 101 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8345 (p) REVERT: L 165 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8348 (tt) REVERT: L 168 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: K 101 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8191 (p) REVERT: K 220 GLU cc_start: 0.8844 (tt0) cc_final: 0.8533 (tt0) REVERT: J 101 SER cc_start: 0.8804 (m) cc_final: 0.8392 (p) REVERT: J 107 GLU cc_start: 0.8514 (tp30) cc_final: 0.8295 (tp30) REVERT: J 149 GLN cc_start: 0.8220 (tt0) cc_final: 0.7982 (tt0) outliers start: 21 outliers final: 15 residues processed: 72 average time/residue: 0.0498 time to fit residues: 5.3127 Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.109643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.097495 restraints weight = 7851.875| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.92 r_work: 0.2943 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5571 Z= 0.172 Angle : 0.524 4.115 7548 Z= 0.283 Chirality : 0.047 0.145 936 Planarity : 0.003 0.031 960 Dihedral : 4.122 14.175 750 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.86 % Allowed : 13.81 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.32), residues: 711 helix: 0.11 (0.63), residues: 72 sheet: 1.03 (0.32), residues: 306 loop : -1.40 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 46 TYR 0.019 0.001 TYR L 43 PHE 0.006 0.001 PHE K 142 HIS 0.002 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5571) covalent geometry : angle 0.52405 ( 7548) hydrogen bonds : bond 0.03951 ( 210) hydrogen bonds : angle 4.80383 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.127 Fit side-chains REVERT: L 101 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8354 (p) REVERT: L 165 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8354 (tt) REVERT: L 168 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: K 101 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8208 (p) REVERT: K 220 GLU cc_start: 0.8816 (tt0) cc_final: 0.8504 (tt0) REVERT: J 101 SER cc_start: 0.8772 (m) cc_final: 0.8395 (p) REVERT: J 107 GLU cc_start: 0.8503 (tp30) cc_final: 0.8302 (tp30) REVERT: J 149 GLN cc_start: 0.8178 (tt0) cc_final: 0.7938 (tt0) outliers start: 18 outliers final: 12 residues processed: 69 average time/residue: 0.0512 time to fit residues: 5.2113 Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN K 75 GLN J 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.094265 restraints weight = 7959.396| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.02 r_work: 0.2903 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5571 Z= 0.257 Angle : 0.604 7.239 7548 Z= 0.322 Chirality : 0.049 0.157 936 Planarity : 0.003 0.036 960 Dihedral : 4.396 15.026 750 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.49 % Allowed : 13.65 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.32), residues: 711 helix: -0.15 (0.62), residues: 72 sheet: 0.92 (0.32), residues: 306 loop : -1.50 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 46 TYR 0.018 0.002 TYR L 43 PHE 0.007 0.001 PHE K 142 HIS 0.003 0.002 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00641 ( 5571) covalent geometry : angle 0.60361 ( 7548) hydrogen bonds : bond 0.04602 ( 210) hydrogen bonds : angle 4.93458 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.222 Fit side-chains REVERT: L 101 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8407 (p) REVERT: L 165 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8353 (tt) REVERT: L 168 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: K 101 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8335 (p) REVERT: K 220 GLU cc_start: 0.8846 (tt0) cc_final: 0.8533 (tt0) REVERT: K 227 SER cc_start: 0.8766 (t) cc_final: 0.8510 (m) REVERT: J 101 SER cc_start: 0.8800 (m) cc_final: 0.8397 (p) REVERT: J 107 GLU cc_start: 0.8559 (tp30) cc_final: 0.8343 (tp30) outliers start: 22 outliers final: 14 residues processed: 72 average time/residue: 0.0479 time to fit residues: 5.2099 Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 75 GLN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.093838 restraints weight = 7970.387| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.02 r_work: 0.2903 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5571 Z= 0.256 Angle : 0.598 5.269 7548 Z= 0.320 Chirality : 0.049 0.156 936 Planarity : 0.003 0.035 960 Dihedral : 4.410 15.155 750 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.02 % Allowed : 13.97 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.32), residues: 711 helix: -0.19 (0.63), residues: 72 sheet: 0.84 (0.32), residues: 306 loop : -1.52 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 46 TYR 0.019 0.002 TYR L 43 PHE 0.008 0.001 PHE K 142 HIS 0.003 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 5571) covalent geometry : angle 0.59846 ( 7548) hydrogen bonds : bond 0.04592 ( 210) hydrogen bonds : angle 4.95194 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.186 Fit side-chains REVERT: L 101 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8409 (p) REVERT: L 165 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8343 (tt) REVERT: L 168 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: K 101 SER cc_start: 0.8819 (OUTLIER) cc_final: 0.8362 (p) REVERT: K 220 GLU cc_start: 0.8842 (tt0) cc_final: 0.8516 (tt0) REVERT: K 227 SER cc_start: 0.8760 (t) cc_final: 0.8507 (m) REVERT: J 101 SER cc_start: 0.8793 (m) cc_final: 0.8389 (p) REVERT: J 107 GLU cc_start: 0.8563 (tp30) cc_final: 0.8348 (tp30) outliers start: 19 outliers final: 13 residues processed: 69 average time/residue: 0.0483 time to fit residues: 5.0619 Evaluate side-chains 70 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 165 LEU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 136 SER Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 75 GLN Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.108408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.095716 restraints weight = 7840.542| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.01 r_work: 0.2933 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5571 Z= 0.152 Angle : 0.517 7.229 7548 Z= 0.281 Chirality : 0.047 0.148 936 Planarity : 0.003 0.030 960 Dihedral : 4.124 14.575 750 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.70 % Allowed : 14.44 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.32), residues: 711 helix: 0.07 (0.63), residues: 72 sheet: 0.89 (0.32), residues: 306 loop : -1.41 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 46 TYR 0.019 0.001 TYR L 43 PHE 0.006 0.001 PHE K 142 HIS 0.002 0.001 HIS L 118 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 5571) covalent geometry : angle 0.51684 ( 7548) hydrogen bonds : bond 0.03796 ( 210) hydrogen bonds : angle 4.83647 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.99 seconds wall clock time: 21 minutes 55.34 seconds (1315.34 seconds total)