Starting phenix.real_space_refine on Thu Mar 6 08:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a03_15046/03_2025/8a03_15046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a03_15046/03_2025/8a03_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_2025/8a03_15046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2025/8a03_15046.map" model { file = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2025/8a03_15046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a03_15046/03_2025/8a03_15046.cif" } resolution = 3.2 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5511 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" 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: J, L Time building chain proxies: 3.38, per 1000 atoms: 0.61 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: 1.31 Conformation dependent library (CDL) restraints added in 691.4 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: 0.76 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: 1.41 Time building geometry restraints manager: 1.56 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: 0.04 Found NCS groups: ncs_group { reference = chain 'K' 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- 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= 0.110 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 (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: 0.63 (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 HIS 0.000 0.000 HIS K 118 PHE 0.004 0.001 PHE L 231 TYR 0.005 0.001 TYR L 43 ARG 0.003 0.001 ARG J 46 *********************** 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 : 0.648 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: 0.1544 time to fit residues: 24.1182 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104356 restraints weight = 7564.635| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.94 r_work: 0.3019 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1408 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= 0.252 Angle : 0.516 5.097 7548 Z= 0.274 Chirality : 0.047 0.144 936 Planarity : 0.003 0.030 960 Dihedral : 3.635 10.744 750 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.90 % Allowed : 6.35 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.33), residues: 711 helix: 0.68 (0.65), residues: 72 sheet: 1.39 (0.32), residues: 312 loop : -0.97 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.008 0.001 PHE J 142 TYR 0.018 0.002 TYR L 43 ARG 0.005 0.001 ARG K 46 *********************** 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 81 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.670 Fit side-chains REVERT: L 152 ASP cc_start: 0.8057 (p0) cc_final: 0.7823 (p0) REVERT: L 225 GLN cc_start: 0.8220 (mt0) cc_final: 0.7935 (mt0) REVERT: K 220 GLU cc_start: 0.8730 (tt0) cc_final: 0.8526 (tt0) REVERT: J 101 SER cc_start: 0.8575 (m) cc_final: 0.8178 (p) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.1538 time to fit residues: 16.6649 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 : 0.654 ------------------------------------------------------------------------------- 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 25 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 GLN L 134 GLN K 75 GLN J 16 GLN J 75 GLN J 134 GLN J 225 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.097409 restraints weight = 7742.752| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.03 r_work: 0.2977 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5571 Z= 0.312 Angle : 0.546 4.860 7548 Z= 0.291 Chirality : 0.048 0.148 936 Planarity : 0.003 0.034 960 Dihedral : 4.034 13.031 750 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.22 % Allowed : 11.11 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.32), residues: 711 helix: 0.22 (0.63), residues: 72 sheet: 1.35 (0.32), residues: 291 loop : -1.17 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 118 PHE 0.007 0.001 PHE L 142 TYR 0.013 0.001 TYR L 43 ARG 0.007 0.001 ARG J 46 *********************** 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 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.862 Fit side-chains REVERT: L 146 ILE cc_start: 0.8438 (pt) cc_final: 0.8097 (mt) REVERT: L 168 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: L 225 GLN cc_start: 0.8337 (mt0) cc_final: 0.8127 (mt0) REVERT: K 220 GLU cc_start: 0.8885 (tt0) cc_final: 0.8592 (tt0) REVERT: J 101 SER cc_start: 0.8674 (m) cc_final: 0.8289 (p) REVERT: J 140 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8455 (mp0) outliers start: 14 outliers final: 12 residues processed: 66 average time/residue: 0.1473 time to fit residues: 14.7009 Evaluate side-chains 59 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 0.0770 chunk 7 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.115506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102495 restraints weight = 7693.160| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.05 r_work: 0.3005 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1821 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= 0.110 Angle : 0.429 3.819 7548 Z= 0.233 Chirality : 0.046 0.132 936 Planarity : 0.003 0.022 960 Dihedral : 3.506 11.976 750 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.43 % Allowed : 12.38 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.33), residues: 711 helix: 0.89 (0.67), residues: 72 sheet: 1.39 (0.32), residues: 306 loop : -1.10 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS L 118 PHE 0.004 0.001 PHE J 231 TYR 0.013 0.001 TYR L 43 ARG 0.005 0.001 ARG J 46 *********************** 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 72 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.571 Fit side-chains REVERT: K 220 GLU cc_start: 0.8844 (tt0) cc_final: 0.8602 (tt0) REVERT: J 101 SER cc_start: 0.8620 (m) cc_final: 0.8150 (p) REVERT: J 140 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8476 (mp0) REVERT: J 149 GLN cc_start: 0.8108 (tt0) cc_final: 0.7892 (tt0) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.1072 time to fit residues: 11.4312 Evaluate side-chains 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 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 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 overall best weight: 6.7388 ------------------------------------------------------------------------------- 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 = 0.3146 r_free = 0.3146 target = 0.106707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.093915 restraints weight = 7884.990| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.02 r_work: 0.2896 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.059 5571 Z= 0.624 Angle : 0.713 5.892 7548 Z= 0.374 Chirality : 0.053 0.176 936 Planarity : 0.004 0.046 960 Dihedral : 4.657 15.469 750 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.17 % Allowed : 13.02 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.31), residues: 711 helix: -0.22 (0.60), residues: 72 sheet: 0.99 (0.32), residues: 306 loop : -1.54 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS L 118 PHE 0.011 0.002 PHE K 142 TYR 0.018 0.002 TYR L 43 ARG 0.004 0.001 ARG J 46 *********************** 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 77 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.639 Fit side-chains REVERT: L 101 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8407 (p) REVERT: L 165 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8389 (tt) REVERT: L 168 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: K 220 GLU cc_start: 0.8852 (tt0) cc_final: 0.8501 (tt0) REVERT: K 227 SER cc_start: 0.8778 (t) cc_final: 0.8536 (m) REVERT: J 101 SER cc_start: 0.8853 (m) cc_final: 0.8442 (p) REVERT: J 107 GLU cc_start: 0.8593 (tp30) cc_final: 0.8392 (tp30) outliers start: 20 outliers final: 14 residues processed: 73 average time/residue: 0.1316 time to fit residues: 13.7868 Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR 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 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 127 ASN Chi-restraints excluded: chain J residue 164 ASP 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 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.111469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098521 restraints weight = 7659.921| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.02 r_work: 0.2953 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5571 Z= 0.125 Angle : 0.445 3.774 7548 Z= 0.243 Chirality : 0.046 0.134 936 Planarity : 0.003 0.024 960 Dihedral : 3.760 13.589 750 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.11 % Allowed : 15.24 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.32), residues: 711 helix: 0.54 (0.65), residues: 72 sheet: 1.13 (0.32), residues: 306 loop : -1.28 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS K 118 PHE 0.005 0.001 PHE L 142 TYR 0.019 0.001 TYR L 43 ARG 0.004 0.001 ARG J 46 *********************** 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 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.632 Fit side-chains REVERT: L 100 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8175 (mt-10) REVERT: L 101 SER cc_start: 0.8705 (m) cc_final: 0.8323 (p) REVERT: L 168 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: K 220 GLU cc_start: 0.8818 (tt0) cc_final: 0.8546 (tt0) REVERT: J 101 SER cc_start: 0.8662 (m) cc_final: 0.8245 (p) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.1252 time to fit residues: 11.0852 Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 ASN 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 101 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 48 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 0.0050 overall best weight: 5.4002 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.107819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095690 restraints weight = 7916.198| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.92 r_work: 0.2908 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 5571 Z= 0.505 Angle : 0.641 5.101 7548 Z= 0.339 Chirality : 0.051 0.147 936 Planarity : 0.004 0.035 960 Dihedral : 4.502 14.901 750 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.17 % Allowed : 14.29 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.31), residues: 711 helix: -0.18 (0.62), residues: 72 sheet: 0.92 (0.32), residues: 306 loop : -1.52 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 118 PHE 0.009 0.001 PHE K 142 TYR 0.018 0.002 TYR L 43 ARG 0.004 0.001 ARG J 46 *********************** 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 73 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.660 Fit side-chains REVERT: L 101 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8440 (p) REVERT: L 165 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8402 (tt) REVERT: L 168 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: K 101 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8301 (p) REVERT: K 220 GLU cc_start: 0.8865 (tt0) cc_final: 0.8539 (tt0) REVERT: K 227 SER cc_start: 0.8795 (t) cc_final: 0.8544 (m) REVERT: J 101 SER cc_start: 0.8823 (m) cc_final: 0.8449 (p) REVERT: J 107 GLU cc_start: 0.8399 (tp30) cc_final: 0.8137 (tp30) outliers start: 20 outliers final: 10 residues processed: 68 average time/residue: 0.1153 time to fit residues: 11.7003 Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 45 GLU 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 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 43 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.109457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096770 restraints weight = 7721.927| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.00 r_work: 0.2955 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5571 Z= 0.187 Angle : 0.486 6.477 7548 Z= 0.265 Chirality : 0.046 0.138 936 Planarity : 0.003 0.025 960 Dihedral : 4.009 14.001 750 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.90 % Allowed : 15.40 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.32), residues: 711 helix: 0.27 (0.64), residues: 72 sheet: 1.00 (0.32), residues: 306 loop : -1.35 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.004 0.001 PHE L 142 TYR 0.019 0.001 TYR L 43 ARG 0.004 0.000 ARG J 46 *********************** 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 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.593 Fit side-chains REVERT: L 101 SER cc_start: 0.8811 (m) cc_final: 0.8377 (p) REVERT: L 168 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8230 (tt0) REVERT: K 220 GLU cc_start: 0.8832 (tt0) cc_final: 0.8521 (tt0) REVERT: J 101 SER cc_start: 0.8777 (m) cc_final: 0.8345 (p) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.1155 time to fit residues: 9.9566 Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 GLN Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain J residue 1 MET 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 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 48 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.113850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101675 restraints weight = 7675.334| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.92 r_work: 0.2970 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5571 Z= 0.144 Angle : 0.450 5.765 7548 Z= 0.246 Chirality : 0.045 0.132 936 Planarity : 0.003 0.024 960 Dihedral : 3.731 13.246 750 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.22 % Allowed : 14.92 % 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 (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: 0.05 (0.32), residues: 711 helix: 0.58 (0.65), residues: 72 sheet: 1.14 (0.32), residues: 306 loop : -1.21 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 118 PHE 0.004 0.001 PHE K 142 TYR 0.006 0.001 TYR K 43 ARG 0.005 0.001 ARG J 46 *********************** 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 70 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.585 Fit side-chains REVERT: L 101 SER cc_start: 0.8759 (m) cc_final: 0.8374 (p) REVERT: L 165 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8251 (tt) REVERT: L 168 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: K 220 GLU cc_start: 0.8740 (tt0) cc_final: 0.8417 (tt0) REVERT: J 101 SER cc_start: 0.8637 (m) cc_final: 0.8253 (p) outliers start: 14 outliers final: 8 residues processed: 67 average time/residue: 0.1164 time to fit residues: 11.5825 Evaluate side-chains 71 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 141 GLU 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 74 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 48 ASN Chi-restraints excluded: chain J residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.095117 restraints weight = 7816.147| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.02 r_work: 0.2910 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5571 Z= 0.307 Angle : 0.537 4.421 7548 Z= 0.289 Chirality : 0.048 0.141 936 Planarity : 0.003 0.026 960 Dihedral : 4.123 13.921 750 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.22 % Allowed : 15.08 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.32), residues: 711 helix: 0.16 (0.63), residues: 72 sheet: 1.04 (0.32), residues: 306 loop : -1.31 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 118 PHE 0.006 0.001 PHE K 142 TYR 0.018 0.001 TYR L 43 ARG 0.004 0.001 ARG J 46 ********************** 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 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.652 Fit side-chains REVERT: L 87 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: L 101 SER cc_start: 0.8832 (m) cc_final: 0.8383 (p) REVERT: L 165 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8315 (tt) REVERT: L 168 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: K 220 GLU cc_start: 0.8886 (tt0) cc_final: 0.8547 (tt0) REVERT: K 227 SER cc_start: 0.8809 (t) cc_final: 0.8411 (m) REVERT: J 101 SER cc_start: 0.8800 (m) cc_final: 0.8367 (p) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 0.1154 time to fit residues: 10.8447 Evaluate side-chains 63 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 141 GLU 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 45 GLU Chi-restraints excluded: chain K residue 74 THR 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 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100641 restraints weight = 7728.446| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.93 r_work: 0.2950 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5571 Z= 0.176 Angle : 0.474 5.784 7548 Z= 0.259 Chirality : 0.046 0.136 936 Planarity : 0.003 0.024 960 Dihedral : 3.887 13.577 750 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.75 % Allowed : 15.71 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.32), residues: 711 helix: 0.43 (0.64), residues: 72 sheet: 1.09 (0.32), residues: 306 loop : -1.22 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 118 PHE 0.005 0.001 PHE L 142 TYR 0.018 0.001 TYR L 43 ARG 0.004 0.001 ARG J 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.48 seconds wall clock time: 41 minutes 57.60 seconds (2517.60 seconds total)