Starting phenix.real_space_refine on Sat Apr 26 15:45:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gzw_51735/04_2025/9gzw_51735.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gzw_51735/04_2025/9gzw_51735.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/9gzw_51735/04_2025/9gzw_51735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gzw_51735/04_2025/9gzw_51735.map" model { file = "/net/cci-nas-00/data/ceres_data/9gzw_51735/04_2025/9gzw_51735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gzw_51735/04_2025/9gzw_51735.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 1332 2.51 5 N 384 2.21 5 O 444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 2160 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 179 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} 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: 1.90, per 1000 atoms: 0.88 Number of scatterers: 2160 At special positions: 0 Unit cell: (72.265, 70.03, 43.955, 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 444 8.00 N 384 7.00 C 1332 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: 0.63 Conformation dependent library (CDL) restraints added in 301.8 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 58.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 22 removed outlier: 6.306A pdb=" N PHE A 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS C 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 17 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N SER C 20 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 19 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ASN C 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN A 21 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE C 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N HIS E 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 17 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N SER E 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER C 19 " --> pdb=" O SER E 20 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN E 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C 21 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE E 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N HIS G 18 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL E 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER G 20 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER E 19 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASN G 22 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN E 21 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE G 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N HIS I 18 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL G 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N SER I 20 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER G 19 " --> pdb=" O SER I 20 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ASN I 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN G 21 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE I 15 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS K 18 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL I 17 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER K 20 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER I 19 " --> pdb=" O SER K 20 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN K 22 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN I 21 " --> pdb=" O ASN K 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.493A pdb=" N LEU A 27 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR C 30 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 29 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 27 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR E 30 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER C 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL E 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 27 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR G 30 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER E 29 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL G 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASN E 31 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU G 27 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR I 30 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER G 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL I 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN G 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU I 27 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR K 30 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER I 29 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL K 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASN I 31 " --> pdb=" O VAL K 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 15 through 22 removed outlier: 6.263A pdb=" N PHE B 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS D 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 17 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER D 20 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 19 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN D 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN B 21 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE D 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS F 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 17 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER F 20 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER D 19 " --> pdb=" O SER F 20 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASN F 22 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN D 21 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE F 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N HIS H 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER H 20 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER F 19 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ASN H 22 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN F 21 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE H 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N HIS J 18 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL H 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER J 20 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER H 19 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ASN J 22 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN H 21 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N PHE J 15 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N HIS L 18 " --> pdb=" O PHE J 15 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL J 17 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER L 20 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER J 19 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ASN L 22 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 6.811A 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: 6.496A pdb=" N LEU B 27 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR D 30 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER B 29 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL D 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU D 27 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR F 30 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER D 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL F 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN D 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU F 27 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR H 30 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER F 29 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL H 32 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN F 31 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU H 27 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR J 30 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER H 29 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL J 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN H 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU J 27 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR L 30 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER J 29 " --> pdb=" O THR L 30 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL L 32 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN J 31 " --> pdb=" O VAL L 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 No hydrogen bonds 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: 0.10 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 348 1.29 - 1.35: 368 1.35 - 1.42: 269 1.42 - 1.48: 359 1.48 - 1.54: 840 Bond restraints: 2184 Sorted by residual: bond pdb=" N GLY E 24 " pdb=" CA GLY E 24 " ideal model delta sigma weight residual 1.456 1.450 0.006 1.16e-02 7.43e+03 2.29e-01 bond pdb=" CE1 PHE F 15 " pdb=" CZ PHE F 15 " ideal model delta sigma weight residual 1.382 1.368 0.014 3.00e-02 1.11e+03 2.06e-01 bond pdb=" CE1 PHE E 15 " pdb=" CZ PHE E 15 " ideal model delta sigma weight residual 1.382 1.369 0.013 3.00e-02 1.11e+03 1.98e-01 bond pdb=" CE1 PHE D 15 " pdb=" CZ PHE D 15 " ideal model delta sigma weight residual 1.382 1.369 0.013 3.00e-02 1.11e+03 1.95e-01 bond pdb=" CE1 PHE H 15 " pdb=" CZ PHE H 15 " ideal model delta sigma weight residual 1.382 1.369 0.013 3.00e-02 1.11e+03 1.95e-01 ... (remaining 2179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 2801 1.62 - 3.24: 139 3.24 - 4.86: 12 4.86 - 6.48: 0 6.48 - 8.10: 12 Bond angle restraints: 2964 Sorted by residual: angle pdb=" CA LEU L 16 " pdb=" CB LEU L 16 " pdb=" CG LEU L 16 " ideal model delta sigma weight residual 116.30 124.40 -8.10 3.50e+00 8.16e-02 5.36e+00 angle pdb=" CA LEU J 16 " pdb=" CB LEU J 16 " pdb=" CG LEU J 16 " ideal model delta sigma weight residual 116.30 124.39 -8.09 3.50e+00 8.16e-02 5.35e+00 angle pdb=" CA LEU I 16 " pdb=" CB LEU I 16 " pdb=" CG LEU I 16 " ideal model delta sigma weight residual 116.30 124.39 -8.09 3.50e+00 8.16e-02 5.34e+00 angle pdb=" CA LEU D 16 " pdb=" CB LEU D 16 " pdb=" CG LEU D 16 " ideal model delta sigma weight residual 116.30 124.39 -8.09 3.50e+00 8.16e-02 5.34e+00 angle pdb=" CA LEU E 16 " pdb=" CB LEU E 16 " pdb=" CG LEU E 16 " ideal model delta sigma weight residual 116.30 124.39 -8.09 3.50e+00 8.16e-02 5.34e+00 ... (remaining 2959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.78: 1008 6.78 - 13.56: 96 13.56 - 20.34: 24 20.34 - 27.12: 48 27.12 - 33.90: 36 Dihedral angle restraints: 1212 sinusoidal: 396 harmonic: 816 Sorted by residual: dihedral pdb=" CA LEU L 27 " pdb=" CB LEU L 27 " pdb=" CG LEU L 27 " pdb=" CD1 LEU L 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.02 32.98 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" CA LEU G 27 " pdb=" CB LEU G 27 " pdb=" CG LEU G 27 " pdb=" CD1 LEU G 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.03 32.97 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" CA LEU K 27 " pdb=" CB LEU K 27 " pdb=" CG LEU K 27 " pdb=" CD1 LEU K 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.04 32.96 3 1.50e+01 4.44e-03 5.47e+00 ... (remaining 1209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 225 0.040 - 0.079: 87 0.079 - 0.119: 24 0.119 - 0.158: 0 0.158 - 0.198: 12 Chirality restraints: 348 Sorted by residual: chirality pdb=" CA PHE J 15 " pdb=" N PHE J 15 " pdb=" C PHE J 15 " pdb=" CB PHE J 15 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA PHE F 15 " pdb=" N PHE F 15 " pdb=" C PHE F 15 " pdb=" CB PHE F 15 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA PHE K 15 " pdb=" N PHE K 15 " pdb=" C PHE K 15 " pdb=" CB PHE K 15 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.60e-01 ... (remaining 345 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 15 " 0.002 2.00e-02 2.50e+03 1.84e-02 5.95e+00 pdb=" CG PHE J 15 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE J 15 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE J 15 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE J 15 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE J 15 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 15 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " -0.002 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE I 15 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 15 " -0.002 2.00e-02 2.50e+03 1.84e-02 5.90e+00 pdb=" CG PHE C 15 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 15 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 15 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 15 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 15 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 15 " 0.001 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 2.67 - 3.12: 1634 3.12 - 3.56: 2123 3.56 - 4.01: 3245 4.01 - 4.45: 3789 4.45 - 4.90: 7184 Nonbonded interactions: 17975 Sorted by model distance: nonbonded pdb=" N NH2 H 38 " pdb=" O TYR J 37 " model vdw 2.673 3.120 nonbonded pdb=" N SER B 34 " pdb=" OG SER B 34 " model vdw 2.691 2.496 nonbonded pdb=" N SER E 34 " pdb=" OG SER E 34 " model vdw 2.692 2.496 nonbonded pdb=" N SER I 34 " pdb=" OG SER I 34 " model vdw 2.692 2.496 nonbonded pdb=" N SER K 34 " pdb=" OG SER K 34 " model vdw 2.692 2.496 ... (remaining 17970 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: 1.540 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.250 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.008 0.102 2196 Z= 0.758 Angle : 0.850 8.102 2964 Z= 0.419 Chirality : 0.058 0.198 348 Planarity : 0.004 0.018 384 Dihedral : 11.342 33.900 684 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 9.52 % Favored : 85.71 % 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: -2.72 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 18 PHE 0.033 0.008 PHE J 15 TYR 0.009 0.002 TYR D 37 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 2184) covalent geometry : angle 0.84972 ( 2964) Misc. bond : bond 0.10147 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.256 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 29 average time/residue: 0.1379 time to fit residues: 4.8843 Evaluate side-chains 25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F 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 34 SER Chi-restraints excluded: chain L residue 34 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 35 ASN E 35 ASN F 21 ASN G 21 ASN G 35 ASN H 35 ASN I 35 ASN J 35 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.100578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.077098 restraints weight = 2693.359| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3260 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 2196 Z= 0.326 Angle : 0.682 5.745 2964 Z= 0.342 Chirality : 0.055 0.120 348 Planarity : 0.003 0.007 384 Dihedral : 5.291 21.188 296 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.40 % Allowed : 3.17 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.57 (0.28), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 18 PHE 0.009 0.003 PHE K 15 TYR 0.004 0.001 TYR J 37 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 2184) covalent geometry : angle 0.68228 ( 2964) Misc. bond : bond 0.00223 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.238 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 3 average time/residue: 0.1722 time to fit residues: 0.9538 Evaluate side-chains 3 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 0.0570 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 ASN F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.102670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.079243 restraints weight = 2696.895| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.94 r_work: 0.3295 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2196 Z= 0.126 Angle : 0.516 5.064 2964 Z= 0.243 Chirality : 0.046 0.113 348 Planarity : 0.001 0.004 384 Dihedral : 3.647 7.503 288 Min Nonbonded Distance : 2.694 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 3.57 % Favored : 95.63 % 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: -3.45 (0.30), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.23), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 18 PHE 0.008 0.002 PHE F 15 TYR 0.002 0.000 TYR F 37 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 2184) covalent geometry : angle 0.51609 ( 2964) Misc. bond : bond 0.00076 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 5 time to evaluate : 0.243 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 7 average time/residue: 0.1782 time to fit residues: 1.7745 Evaluate side-chains 6 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain G residue 34 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 2 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN E 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.099000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076217 restraints weight = 2939.997| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.99 r_work: 0.3254 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 2196 Z= 0.343 Angle : 0.620 4.698 2964 Z= 0.321 Chirality : 0.051 0.116 348 Planarity : 0.003 0.007 384 Dihedral : 4.784 8.812 288 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 5.95 % Favored : 93.25 % 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: -4.26 (0.32), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.25), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.013 0.003 PHE F 15 TYR 0.006 0.001 TYR A 37 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 2184) covalent geometry : angle 0.61998 ( 2964) Misc. bond : bond 0.00182 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 3 time to evaluate : 0.251 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 5 average time/residue: 0.1616 time to fit residues: 1.2876 Evaluate side-chains 4 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 ASN F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.076604 restraints weight = 3544.454| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.07 r_work: 0.3268 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2196 Z= 0.205 Angle : 0.503 4.073 2964 Z= 0.257 Chirality : 0.046 0.115 348 Planarity : 0.002 0.005 384 Dihedral : 4.081 8.568 288 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 8.33 % Favored : 90.87 % 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: -4.15 (0.34), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.26), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS L 18 PHE 0.011 0.002 PHE F 15 TYR 0.005 0.001 TYR B 37 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 2184) covalent geometry : angle 0.50328 ( 2964) Misc. bond : bond 0.00118 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 3 time to evaluate : 0.240 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 5 average time/residue: 0.1633 time to fit residues: 1.2893 Evaluate side-chains 5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 3 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.0770 chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3781 r_free = 0.3781 target = 0.099564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076735 restraints weight = 3349.702| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.02 r_work: 0.3268 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2196 Z= 0.178 Angle : 0.489 4.094 2964 Z= 0.248 Chirality : 0.046 0.115 348 Planarity : 0.001 0.005 384 Dihedral : 3.952 8.279 288 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 9.52 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.27), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 18 PHE 0.010 0.002 PHE L 15 TYR 0.005 0.001 TYR I 37 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 2184) covalent geometry : angle 0.48948 ( 2964) Misc. bond : bond 0.00101 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2 time to evaluate : 0.245 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 4 average time/residue: 0.1409 time to fit residues: 1.0382 Evaluate side-chains 4 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 2 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.099449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.076185 restraints weight = 3220.181| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.01 r_work: 0.3259 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2196 Z= 0.183 Angle : 0.487 3.865 2964 Z= 0.249 Chirality : 0.046 0.115 348 Planarity : 0.001 0.004 384 Dihedral : 3.985 8.285 288 Min Nonbonded Distance : 2.675 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.19 % Allowed : 10.71 % Favored : 88.10 % 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: -4.05 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 18 PHE 0.009 0.002 PHE L 15 TYR 0.005 0.001 TYR I 37 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 2184) covalent geometry : angle 0.48715 ( 2964) Misc. bond : bond 0.00100 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 2 time to evaluate : 0.227 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 5 average time/residue: 0.1176 time to fit residues: 1.1301 Evaluate side-chains 5 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 2 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076014 restraints weight = 3805.162| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.09 r_work: 0.3243 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.004 0.018 2196 Z= 0.189 Angle : 0.486 3.810 2964 Z= 0.251 Chirality : 0.046 0.114 348 Planarity : 0.002 0.004 384 Dihedral : 4.007 8.452 288 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.19 % Allowed : 11.11 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.37), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 18 PHE 0.009 0.002 PHE F 15 TYR 0.006 0.001 TYR B 37 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2184) covalent geometry : angle 0.48557 ( 2964) Misc. bond : bond 0.00109 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 3 time to evaluate : 0.229 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 6 average time/residue: 0.1402 time to fit residues: 1.3407 Evaluate side-chains 6 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 3 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 0.0020 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.075310 restraints weight = 3873.965| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.12 r_work: 0.3232 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2196 Z= 0.200 Angle : 0.491 3.776 2964 Z= 0.256 Chirality : 0.046 0.114 348 Planarity : 0.002 0.005 384 Dihedral : 4.037 8.356 288 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.19 % Allowed : 11.51 % Favored : 87.30 % 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: -4.14 (0.37), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 18 PHE 0.010 0.002 PHE I 15 TYR 0.006 0.001 TYR B 37 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 2184) covalent geometry : angle 0.49070 ( 2964) Misc. bond : bond 0.00117 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.229 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 7 average time/residue: 0.1541 time to fit residues: 1.5708 Evaluate side-chains 7 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.099225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075638 restraints weight = 3350.062| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.99 r_work: 0.3246 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2196 Z= 0.187 Angle : 0.483 3.656 2964 Z= 0.252 Chirality : 0.046 0.113 348 Planarity : 0.002 0.005 384 Dihedral : 3.947 8.387 288 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.19 % Allowed : 11.51 % Favored : 87.30 % 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: -4.19 (0.37), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 18 PHE 0.010 0.002 PHE L 15 TYR 0.006 0.001 TYR B 37 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 2184) covalent geometry : angle 0.48306 ( 2964) Misc. bond : bond 0.00112 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.270 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 10 average time/residue: 0.1818 time to fit residues: 2.4073 Evaluate side-chains 10 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074029 restraints weight = 3325.993| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.00 r_work: 0.3213 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 2196 Z= 0.345 Angle : 0.579 3.827 2964 Z= 0.311 Chirality : 0.048 0.114 348 Planarity : 0.003 0.006 384 Dihedral : 4.542 9.380 288 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.19 % Allowed : 11.51 % Favored : 87.30 % 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: -4.25 (0.36), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.28), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 18 PHE 0.012 0.003 PHE L 15 TYR 0.010 0.002 TYR B 37 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 2184) covalent geometry : angle 0.57884 ( 2964) Misc. bond : bond 0.00202 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1592.81 seconds wall clock time: 28 minutes 25.75 seconds (1705.75 seconds total)