Starting phenix.real_space_refine on Sat Apr 26 15:32:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzp_51730/04_2025/9gzp_51730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzp_51730/04_2025/9gzp_51730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gzp_51730/04_2025/9gzp_51730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzp_51730/04_2025/9gzp_51730.map" model { file = "/net/cci-nas-00/data/ceres_data/9gzp_51730/04_2025/9gzp_51730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzp_51730/04_2025/9gzp_51730.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 1284 2.51 5 N 360 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 171 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.63, per 1000 atoms: 0.79 Number of scatterers: 2064 At special positions: 0 Unit cell: (73.755, 61.09, 44.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 360 7.00 C 1284 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 262.0 milliseconds 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 504 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 56.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.592A pdb=" N VAL C 17 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER E 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N SER C 19 " --> pdb=" O SER E 20 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASN E 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C 21 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER I 20 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER G 19 " --> pdb=" O SER I 20 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASN I 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN G 21 " --> pdb=" O ASN I 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.386A pdb=" N LEU C 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR E 30 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N SER C 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL E 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU G 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N THR I 30 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER G 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL I 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN G 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU I 27 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR K 30 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER I 29 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL K 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN I 31 " --> pdb=" O VAL K 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 22 removed outlier: 6.615A pdb=" N VAL B 17 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER D 20 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER B 19 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASN D 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B 21 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 17 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N SER F 20 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER D 19 " --> pdb=" O SER F 20 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ASN F 22 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN D 21 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER H 20 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER F 19 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN H 22 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN F 21 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL H 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER J 20 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER H 19 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN J 22 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN H 21 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL J 17 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER L 20 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER J 19 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASN L 22 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN J 21 " --> pdb=" O ASN L 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 26 through 33 removed outlier: 6.505A pdb=" N LEU D 27 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N THR F 30 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER D 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL F 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN D 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU H 27 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N THR J 30 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER H 29 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL J 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN H 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU J 27 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR L 30 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER J 29 " --> pdb=" O THR L 30 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL L 32 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN J 31 " --> pdb=" O VAL L 32 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.47 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 324 1.29 - 1.35: 336 1.35 - 1.41: 264 1.41 - 1.47: 372 1.47 - 1.54: 792 Bond restraints: 2088 Sorted by residual: bond pdb=" CG LEU K 16 " pdb=" CD2 LEU K 16 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" CG LEU I 16 " pdb=" CD2 LEU I 16 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.50e+00 bond pdb=" CG LEU E 16 " pdb=" CD2 LEU E 16 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.47e+00 bond pdb=" CG LEU H 16 " pdb=" CD2 LEU H 16 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.47e+00 bond pdb=" CG LEU L 16 " pdb=" CD2 LEU L 16 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.46e+00 ... (remaining 2083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 2330 1.02 - 2.05: 374 2.05 - 3.07: 80 3.07 - 4.10: 12 4.10 - 5.12: 36 Bond angle restraints: 2832 Sorted by residual: angle pdb=" N GLY J 24 " pdb=" CA GLY J 24 " pdb=" C GLY J 24 " ideal model delta sigma weight residual 111.19 116.31 -5.12 1.75e+00 3.27e-01 8.56e+00 angle pdb=" N GLY C 24 " pdb=" CA GLY C 24 " pdb=" C GLY C 24 " ideal model delta sigma weight residual 111.19 116.31 -5.12 1.75e+00 3.27e-01 8.55e+00 angle pdb=" N GLY F 24 " pdb=" CA GLY F 24 " pdb=" C GLY F 24 " ideal model delta sigma weight residual 111.19 116.30 -5.11 1.75e+00 3.27e-01 8.51e+00 angle pdb=" N GLY K 24 " pdb=" CA GLY K 24 " pdb=" C GLY K 24 " ideal model delta sigma weight residual 111.19 116.28 -5.09 1.75e+00 3.27e-01 8.47e+00 angle pdb=" N GLY G 24 " pdb=" CA GLY G 24 " pdb=" C GLY G 24 " ideal model delta sigma weight residual 111.19 116.28 -5.09 1.75e+00 3.27e-01 8.46e+00 ... (remaining 2827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.20: 948 5.20 - 10.40: 72 10.40 - 15.59: 60 15.59 - 20.79: 48 20.79 - 25.99: 24 Dihedral angle restraints: 1152 sinusoidal: 372 harmonic: 780 Sorted by residual: dihedral pdb=" N SER A 20 " pdb=" CA SER A 20 " pdb=" CB SER A 20 " pdb=" OG SER A 20 " ideal model delta sinusoidal sigma weight residual -60.00 -36.97 -23.03 3 1.50e+01 4.44e-03 3.05e+00 dihedral pdb=" N SER G 20 " pdb=" CA SER G 20 " pdb=" CB SER G 20 " pdb=" OG SER G 20 " ideal model delta sinusoidal sigma weight residual -60.00 -36.99 -23.01 3 1.50e+01 4.44e-03 3.04e+00 dihedral pdb=" N SER H 20 " pdb=" CA SER H 20 " pdb=" CB SER H 20 " pdb=" OG SER H 20 " ideal model delta sinusoidal sigma weight residual -60.00 -37.02 -22.98 3 1.50e+01 4.44e-03 3.04e+00 ... (remaining 1149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 270 0.067 - 0.133: 42 0.133 - 0.200: 12 0.200 - 0.266: 0 0.266 - 0.333: 12 Chirality restraints: 336 Sorted by residual: chirality pdb=" CG LEU K 16 " pdb=" CB LEU K 16 " pdb=" CD1 LEU K 16 " pdb=" CD2 LEU K 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CG LEU J 16 " pdb=" CB LEU J 16 " pdb=" CD1 LEU J 16 " pdb=" CD2 LEU J 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CG LEU F 16 " pdb=" CB LEU F 16 " pdb=" CD1 LEU F 16 " pdb=" CD2 LEU F 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 333 not shown) Planarity restraints: 360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 23 " -0.008 2.00e-02 2.50e+03 7.69e-03 1.03e+00 pdb=" CG PHE A 23 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 23 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 23 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 23 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 23 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 23 " -0.008 2.00e-02 2.50e+03 7.67e-03 1.03e+00 pdb=" CG PHE C 23 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE C 23 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 23 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 23 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 23 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 23 " -0.008 2.00e-02 2.50e+03 7.67e-03 1.03e+00 pdb=" CG PHE G 23 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE G 23 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 23 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE G 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 23 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 23 " -0.002 2.00e-02 2.50e+03 ... (remaining 357 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 989 2.94 - 3.43: 1661 3.43 - 3.92: 3505 3.92 - 4.41: 3635 4.41 - 4.90: 6919 Nonbonded interactions: 16709 Sorted by model distance: nonbonded pdb=" OD1 ASN A 35 " pdb=" N SER C 34 " model vdw 2.451 3.120 nonbonded pdb=" N NH2 H 38 " pdb=" O TYR J 37 " model vdw 2.544 3.120 nonbonded pdb=" N NH2 D 38 " pdb=" O TYR F 37 " model vdw 2.550 3.120 nonbonded pdb=" OD1 ASN E 35 " pdb=" N SER G 34 " model vdw 2.585 3.120 nonbonded pdb=" N NH2 I 38 " pdb=" O TYR K 37 " model vdw 2.618 3.120 ... (remaining 16704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = 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: 1.490 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.050 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:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.011 0.103 2100 Z= 0.826 Angle : 0.925 5.119 2832 Z= 0.531 Chirality : 0.082 0.333 336 Planarity : 0.003 0.008 360 Dihedral : 8.569 25.987 648 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -4.08 (0.29), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.22), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS A 18 PHE 0.018 0.004 PHE A 23 TYR 0.012 0.003 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.14231 ( 46) hydrogen bonds : angle 5.83403 ( 138) covalent geometry : bond 0.00749 ( 2088) covalent geometry : angle 0.92525 ( 2832) Misc. bond : bond 0.10275 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1767 time to fit residues: 3.0566 Evaluate side-chains 6 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN D 35 ASN F 35 ASN H 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.100238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086608 restraints weight = 2998.532| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.86 r_work: 0.3563 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2100 Z= 0.277 Angle : 0.639 6.686 2832 Z= 0.346 Chirality : 0.052 0.132 336 Planarity : 0.003 0.006 360 Dihedral : 4.233 12.406 276 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.25 % Allowed : 12.08 % 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: -4.38 (0.29), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.22), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS I 18 PHE 0.010 0.003 PHE J 15 TYR 0.005 0.001 TYR J 37 Details of bonding type rmsd hydrogen bonds : bond 0.02352 ( 46) hydrogen bonds : angle 4.33946 ( 138) covalent geometry : bond 0.00601 ( 2088) covalent geometry : angle 0.63904 ( 2832) Misc. bond : bond 0.00087 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.237 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.1789 time to fit residues: 2.8810 Evaluate side-chains 11 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 20 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN C 35 ASN D 35 ASN E 35 ASN G 35 ASN I 35 ASN J 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.103758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.089338 restraints weight = 2771.925| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.92 r_work: 0.3587 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2100 Z= 0.242 Angle : 0.591 5.871 2832 Z= 0.314 Chirality : 0.048 0.121 336 Planarity : 0.002 0.005 360 Dihedral : 4.151 11.798 276 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % 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: -4.90 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 18 PHE 0.011 0.003 PHE C 23 TYR 0.004 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.02110 ( 46) hydrogen bonds : angle 4.00056 ( 138) covalent geometry : bond 0.00514 ( 2088) covalent geometry : angle 0.59095 ( 2832) Misc. bond : bond 0.00076 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 8 time to evaluate : 0.245 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 12 average time/residue: 0.1717 time to fit residues: 2.6476 Evaluate side-chains 10 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain F residue 20 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN C 35 ASN D 35 ASN F 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.098423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085092 restraints weight = 3026.850| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.84 r_work: 0.3557 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2100 Z= 0.136 Angle : 0.516 5.401 2832 Z= 0.260 Chirality : 0.045 0.119 336 Planarity : 0.001 0.004 360 Dihedral : 3.643 9.994 276 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 11.25 % 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: -4.87 (0.28), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 18 PHE 0.008 0.002 PHE C 23 TYR 0.003 0.001 TYR J 37 Details of bonding type rmsd hydrogen bonds : bond 0.01320 ( 46) hydrogen bonds : angle 3.56302 ( 138) covalent geometry : bond 0.00283 ( 2088) covalent geometry : angle 0.51613 ( 2832) Misc. bond : bond 0.00043 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.195 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 12 average time/residue: 0.1501 time to fit residues: 2.3094 Evaluate side-chains 10 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 5 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 0.0570 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 ASN G 35 ASN I 35 ASN J 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.102544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.087980 restraints weight = 2808.964| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.90 r_work: 0.3557 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2100 Z= 0.278 Angle : 0.566 4.360 2832 Z= 0.309 Chirality : 0.047 0.119 336 Planarity : 0.002 0.005 360 Dihedral : 4.140 11.307 276 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 6.67 % Allowed : 7.08 % Favored : 86.25 % 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: -5.22 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS A 18 PHE 0.012 0.003 PHE G 23 TYR 0.006 0.002 TYR J 37 Details of bonding type rmsd hydrogen bonds : bond 0.02129 ( 46) hydrogen bonds : angle 3.91079 ( 138) covalent geometry : bond 0.00579 ( 2088) covalent geometry : angle 0.56640 ( 2832) Misc. bond : bond 0.00092 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 6 time to evaluate : 0.202 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 22 average time/residue: 0.0969 time to fit residues: 2.8490 Evaluate side-chains 20 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 6 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN C 35 ASN F 35 ASN L 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.102030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.087434 restraints weight = 2795.867| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.87 r_work: 0.3553 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2100 Z= 0.286 Angle : 0.571 4.167 2832 Z= 0.311 Chirality : 0.047 0.117 336 Planarity : 0.002 0.006 360 Dihedral : 4.209 11.019 276 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 6.67 % Allowed : 7.08 % Favored : 86.25 % 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: -5.33 (0.26), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 18 PHE 0.013 0.003 PHE C 23 TYR 0.008 0.002 TYR J 37 Details of bonding type rmsd hydrogen bonds : bond 0.02273 ( 46) hydrogen bonds : angle 3.94945 ( 138) covalent geometry : bond 0.00595 ( 2088) covalent geometry : angle 0.57148 ( 2832) Misc. bond : bond 0.00093 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 5 time to evaluate : 0.225 Fit side-chains outliers start: 16 outliers final: 15 residues processed: 21 average time/residue: 0.0849 time to fit residues: 2.4914 Evaluate side-chains 20 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 5 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN G 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.102559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.087790 restraints weight = 2903.978| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.93 r_work: 0.3554 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2100 Z= 0.236 Angle : 0.542 4.185 2832 Z= 0.291 Chirality : 0.046 0.118 336 Planarity : 0.002 0.005 360 Dihedral : 3.986 10.690 276 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 5.83 % Allowed : 7.08 % Favored : 87.08 % 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: -5.34 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 18 PHE 0.011 0.002 PHE C 23 TYR 0.007 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.01977 ( 46) hydrogen bonds : angle 3.79748 ( 138) covalent geometry : bond 0.00489 ( 2088) covalent geometry : angle 0.54217 ( 2832) Misc. bond : bond 0.00080 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 5 time to evaluate : 0.234 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 19 average time/residue: 0.0969 time to fit residues: 2.5272 Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN D 35 ASN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.103640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.088995 restraints weight = 2813.749| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.91 r_work: 0.3576 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2100 Z= 0.134 Angle : 0.495 4.469 2832 Z= 0.255 Chirality : 0.045 0.117 336 Planarity : 0.001 0.004 360 Dihedral : 3.592 9.746 276 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 7.50 % Favored : 87.50 % 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: -5.16 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 18 PHE 0.008 0.001 PHE K 23 TYR 0.004 0.001 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.01352 ( 46) hydrogen bonds : angle 3.42296 ( 138) covalent geometry : bond 0.00277 ( 2088) covalent geometry : angle 0.49466 ( 2832) Misc. bond : bond 0.00045 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 4 time to evaluate : 0.245 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 16 average time/residue: 0.0939 time to fit residues: 2.1708 Evaluate side-chains 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 4 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 0.0070 chunk 17 optimal weight: 5.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN G 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.101858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086897 restraints weight = 3071.124| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.96 r_work: 0.3549 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 2100 Z= 0.274 Angle : 0.545 3.725 2832 Z= 0.300 Chirality : 0.046 0.116 336 Planarity : 0.002 0.005 360 Dihedral : 4.084 11.040 276 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 5.42 % Allowed : 7.08 % Favored : 87.50 % 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: -5.33 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.013 0.003 PHE G 23 TYR 0.009 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.02075 ( 46) hydrogen bonds : angle 3.82891 ( 138) covalent geometry : bond 0.00573 ( 2088) covalent geometry : angle 0.54525 ( 2832) Misc. bond : bond 0.00094 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.210 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 18 average time/residue: 0.0927 time to fit residues: 2.2911 Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN D 35 ASN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.100468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.085848 restraints weight = 3396.872| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.05 r_work: 0.3571 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 2100 Z= 0.233 Angle : 0.530 3.907 2832 Z= 0.286 Chirality : 0.045 0.117 336 Planarity : 0.002 0.005 360 Dihedral : 3.942 10.784 276 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 5.83 % Allowed : 6.67 % Favored : 87.50 % 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: -5.31 (0.28), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS L 18 PHE 0.011 0.002 PHE C 23 TYR 0.007 0.002 TYR G 37 Details of bonding type rmsd hydrogen bonds : bond 0.01937 ( 46) hydrogen bonds : angle 3.71358 ( 138) covalent geometry : bond 0.00484 ( 2088) covalent geometry : angle 0.53005 ( 2832) Misc. bond : bond 0.00079 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 5 time to evaluate : 0.245 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 19 average time/residue: 0.1527 time to fit residues: 3.8536 Evaluate side-chains 18 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 4 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN F 35 ASN G 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.103207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088470 restraints weight = 3411.831| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.04 r_work: 0.3588 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2100 Z= 0.088 Angle : 0.475 4.524 2832 Z= 0.238 Chirality : 0.044 0.119 336 Planarity : 0.001 0.003 360 Dihedral : 3.332 8.970 276 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 9.17 % Favored : 87.50 % 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: -4.99 (0.28), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.22), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 18 PHE 0.006 0.001 PHE C 23 TYR 0.002 0.001 TYR C 37 Details of bonding type rmsd hydrogen bonds : bond 0.01061 ( 46) hydrogen bonds : angle 3.22367 ( 138) covalent geometry : bond 0.00181 ( 2088) covalent geometry : angle 0.47472 ( 2832) Misc. bond : bond 0.00028 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1371.38 seconds wall clock time: 24 minutes 36.15 seconds (1476.15 seconds total)