Starting phenix.real_space_refine on Wed Sep 17 02:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzp_51730/09_2025/9gzp_51730.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzp_51730/09_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_51730/09_2025/9gzp_51730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzp_51730/09_2025/9gzp_51730.map" model { file = "/net/cci-nas-00/data/ceres_data/9gzp_51730/09_2025/9gzp_51730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzp_51730/09_2025/9gzp_51730.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.41, per 1000 atoms: 0.20 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: 0.27 Conformation dependent library (CDL) restraints added in 49.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.11 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: 0.25 Time building geometry restraints manager: 0.24 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.450 Find NCS groups from input model: 0.010 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:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.012 0.003 TYR G 37 PHE 0.018 0.004 PHE A 23 HIS 0.006 0.004 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00749 ( 2088) covalent geometry : angle 0.92525 ( 2832) hydrogen bonds : bond 0.14231 ( 46) hydrogen bonds : angle 5.83403 ( 138) 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 : 0.086 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0884 time to fit residues: 1.4841 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 : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.101179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.087452 restraints weight = 2950.927| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.88 r_work: 0.3577 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2100 Z= 0.240 Angle : 0.602 6.180 2832 Z= 0.325 Chirality : 0.051 0.129 336 Planarity : 0.003 0.006 360 Dihedral : 4.173 12.204 276 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.25 (0.30), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.23), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR J 37 PHE 0.010 0.002 PHE G 23 HIS 0.005 0.003 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 2088) covalent geometry : angle 0.60244 ( 2832) hydrogen bonds : bond 0.02217 ( 46) hydrogen bonds : angle 4.22671 ( 138) Misc. bond : bond 0.00063 ( 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 9 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1090 time to fit residues: 1.1862 Evaluate side-chains 8 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 E 35 ASN G 35 ASN I 35 ASN J 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.099073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.085831 restraints weight = 3061.645| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.85 r_work: 0.3556 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2100 Z= 0.218 Angle : 0.563 5.808 2832 Z= 0.301 Chirality : 0.047 0.119 336 Planarity : 0.002 0.005 360 Dihedral : 3.993 11.603 276 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 0.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 11.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.71 (0.28), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR J 37 PHE 0.011 0.002 PHE C 23 HIS 0.004 0.002 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 2088) covalent geometry : angle 0.56308 ( 2832) hydrogen bonds : bond 0.01975 ( 46) hydrogen bonds : angle 3.90482 ( 138) Misc. bond : bond 0.00068 ( 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 11 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.081 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 11 average time/residue: 0.0761 time to fit residues: 1.0511 Evaluate side-chains 9 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain J residue 20 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.101295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.086582 restraints weight = 2850.992| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.86 r_work: 0.3538 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.036 2100 Z= 0.425 Angle : 0.696 5.214 2832 Z= 0.385 Chirality : 0.052 0.121 336 Planarity : 0.003 0.008 360 Dihedral : 4.703 12.035 276 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.67 % Allowed : 8.33 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.41 (0.26), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 37 PHE 0.015 0.004 PHE C 23 HIS 0.006 0.004 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00889 ( 2088) covalent geometry : angle 0.69634 ( 2832) hydrogen bonds : bond 0.03167 ( 46) hydrogen bonds : angle 4.64783 ( 138) Misc. bond : bond 0.00142 ( 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 19 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 3 time to evaluate : 0.082 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 19 average time/residue: 0.0366 time to fit residues: 0.9816 Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 3 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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 K residue 34 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 15 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.102756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088084 restraints weight = 2828.233| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.89 r_work: 0.3557 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3537 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= 0.249 Angle : 0.582 5.115 2832 Z= 0.307 Chirality : 0.047 0.119 336 Planarity : 0.002 0.005 360 Dihedral : 4.141 11.278 276 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 : 3.75 % Allowed : 11.25 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.41 (0.26), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR G 37 PHE 0.011 0.002 PHE K 23 HIS 0.004 0.002 HIS L 18 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 2088) covalent geometry : angle 0.58244 ( 2832) hydrogen bonds : bond 0.02167 ( 46) hydrogen bonds : angle 4.07619 ( 138) Misc. bond : bond 0.00082 ( 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 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 7 time to evaluate : 0.076 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 16 average time/residue: 0.0617 time to fit residues: 1.2493 Evaluate side-chains 14 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 7 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 F residue 20 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 E 35 ASN F 35 ASN G 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.102263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.087528 restraints weight = 2835.913| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.90 r_work: 0.3550 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2100 Z= 0.262 Angle : 0.576 4.674 2832 Z= 0.309 Chirality : 0.047 0.118 336 Planarity : 0.002 0.005 360 Dihedral : 4.174 11.146 276 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 6.67 % Allowed : 7.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.41 (0.26), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR C 37 PHE 0.011 0.002 PHE C 23 HIS 0.004 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 2088) covalent geometry : angle 0.57624 ( 2832) hydrogen bonds : bond 0.02134 ( 46) hydrogen bonds : angle 4.02093 ( 138) Misc. bond : bond 0.00094 ( 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 19 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 3 time to evaluate : 0.078 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 19 average time/residue: 0.0294 time to fit residues: 0.8080 Evaluate side-chains 17 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 3 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 15 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: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.086982 restraints weight = 2961.961| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.91 r_work: 0.3553 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3735 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= 0.282 Angle : 0.575 4.498 2832 Z= 0.312 Chirality : 0.047 0.120 336 Planarity : 0.002 0.005 360 Dihedral : 4.190 11.308 276 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 5.83 % Allowed : 8.33 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.45 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.20), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR K 37 PHE 0.012 0.002 PHE G 23 HIS 0.004 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 2088) covalent geometry : angle 0.57535 ( 2832) hydrogen bonds : bond 0.02261 ( 46) hydrogen bonds : angle 4.06071 ( 138) Misc. bond : bond 0.00099 ( 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 : 0.097 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 19 average time/residue: 0.0364 time to fit residues: 0.9336 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 : 0.081 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.102718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.087895 restraints weight = 2937.777| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.94 r_work: 0.3565 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2100 Z= 0.183 Angle : 0.527 4.529 2832 Z= 0.275 Chirality : 0.045 0.120 336 Planarity : 0.001 0.004 360 Dihedral : 3.845 10.487 276 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.17 % Allowed : 9.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.36 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR K 37 PHE 0.009 0.002 PHE K 23 HIS 0.003 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2088) covalent geometry : angle 0.52677 ( 2832) hydrogen bonds : bond 0.01671 ( 46) hydrogen bonds : angle 3.69495 ( 138) Misc. bond : bond 0.00065 ( 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 13 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 3 time to evaluate : 0.066 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 13 average time/residue: 0.0362 time to fit residues: 0.6614 Evaluate side-chains 13 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 3 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.086488 restraints weight = 3359.437| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.00 r_work: 0.3539 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3802 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 : 0.567 4.211 2832 Z= 0.309 Chirality : 0.047 0.121 336 Planarity : 0.002 0.005 360 Dihedral : 4.170 11.298 276 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.58 % Allowed : 9.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.46 (0.27), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.15 (0.21), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 37 PHE 0.012 0.002 PHE G 23 HIS 0.004 0.002 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 2088) covalent geometry : angle 0.56660 ( 2832) hydrogen bonds : bond 0.02206 ( 46) hydrogen bonds : angle 3.95874 ( 138) Misc. bond : bond 0.00104 ( 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 15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 4 time to evaluate : 0.084 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 15 average time/residue: 0.0474 time to fit residues: 0.9742 Evaluate side-chains 15 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 4 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.102536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.087333 restraints weight = 3907.169| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.15 r_work: 0.3548 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2100 Z= 0.166 Angle : 0.516 4.397 2832 Z= 0.268 Chirality : 0.045 0.120 336 Planarity : 0.001 0.004 360 Dihedral : 3.798 10.266 276 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.42 % Allowed : 7.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.34 (0.28), 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 TYR 0.004 0.001 TYR I 37 PHE 0.008 0.002 PHE K 23 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 2088) covalent geometry : angle 0.51560 ( 2832) hydrogen bonds : bond 0.01546 ( 46) hydrogen bonds : angle 3.62049 ( 138) Misc. bond : bond 0.00057 ( 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 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 3 time to evaluate : 0.081 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 16 average time/residue: 0.0371 time to fit residues: 0.8521 Evaluate side-chains 16 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 3 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.102288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.087447 restraints weight = 3010.875| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.93 r_work: 0.3554 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2100 Z= 0.195 Angle : 0.521 4.284 2832 Z= 0.275 Chirality : 0.045 0.118 336 Planarity : 0.002 0.004 360 Dihedral : 3.848 10.620 276 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 7.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.31 (0.28), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.22), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR K 37 PHE 0.010 0.002 PHE C 23 HIS 0.003 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 2088) covalent geometry : angle 0.52084 ( 2832) hydrogen bonds : bond 0.01676 ( 46) hydrogen bonds : angle 3.60229 ( 138) Misc. bond : bond 0.00068 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 738.72 seconds wall clock time: 14 minutes 8.76 seconds (848.76 seconds total)