Starting phenix.real_space_refine on Thu Mar 6 04:26:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol3_16944/03_2025/8ol3_16944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol3_16944/03_2025/8ol3_16944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ol3_16944/03_2025/8ol3_16944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol3_16944/03_2025/8ol3_16944.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol3_16944/03_2025/8ol3_16944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol3_16944/03_2025/8ol3_16944.cif" } resolution = 3.5 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= 0.280 sd= 1.397 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1610 2.51 5 N 410 2.21 5 O 440 1.98 5 H 2500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4970 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.42, per 1000 atoms: 0.49 Number of scatterers: 4970 At special positions: 0 Unit cell: (61.2, 90.576, 39.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 440 8.00 N 410 7.00 C 1610 6.00 H 2500 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 401.2 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 60.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 21 removed outlier: 7.049A pdb=" N VAL C 12 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS A 13 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS C 14 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL E 12 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS C 13 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS E 14 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N HIS G 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS E 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LYS G 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL G 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE G 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE E 19 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL I 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE I 20 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE G 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 8.596A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN G 27 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N SER E 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASN I 27 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N SER G 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.212A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU G 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLY E 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU I 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY G 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.447A pdb=" N VAL E 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 21 removed outlier: 9.222A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL D 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE B 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL F 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N PHE F 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE D 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL H 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE H 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE F 19 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N HIS J 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N HIS H 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS J 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN H 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL J 18 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE J 20 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE H 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 27 removed outlier: 8.627A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN F 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N SER D 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N VAL F 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN H 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER F 26 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL H 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN J 27 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N SER H 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.242A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU F 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY D 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE F 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU H 34 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY F 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE H 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU J 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY H 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 32 hydrogen bonds defined for protein. 96 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.17: 2470 1.17 - 1.50: 1420 1.50 - 1.83: 1100 1.83 - 2.16: 10 2.16 - 2.49: 10 Bond restraints: 5010 Sorted by residual: bond pdb=" CE1 HIS H 13 " pdb=" HE1 HIS H 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 bond pdb=" CE1 HIS G 13 " pdb=" HD2 HIS G 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 bond pdb=" CE1 HIS F 13 " pdb=" HD2 HIS F 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 bond pdb=" CE1 HIS A 13 " pdb=" HE1 HIS A 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 bond pdb=" CE1 HIS E 13 " pdb=" HD2 HIS E 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 ... (remaining 5005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 22.09: 9010 22.09 - 44.17: 20 44.17 - 66.26: 0 66.26 - 88.35: 0 88.35 - 110.44: 30 Bond angle restraints: 9060 Sorted by residual: angle pdb=" CG HIS J 13 " pdb=" CD2 HIS J 13 " pdb=" HD1 HIS J 13 " ideal model delta sigma weight residual 126.40 15.96 110.44 3.00e+00 1.11e-01 1.36e+03 angle pdb=" CG HIS C 13 " pdb=" CD2 HIS C 13 " pdb=" HD1 HIS C 13 " ideal model delta sigma weight residual 126.40 15.97 110.43 3.00e+00 1.11e-01 1.35e+03 angle pdb=" CG HIS D 13 " pdb=" CD2 HIS D 13 " pdb=" HD1 HIS D 13 " ideal model delta sigma weight residual 126.40 15.98 110.42 3.00e+00 1.11e-01 1.35e+03 angle pdb=" CG HIS H 13 " pdb=" CD2 HIS H 13 " pdb=" HD2 HIS H 13 " ideal model delta sigma weight residual 126.40 15.98 110.42 3.00e+00 1.11e-01 1.35e+03 angle pdb=" CG HIS F 13 " pdb=" CD2 HIS F 13 " pdb=" HD1 HIS F 13 " ideal model delta sigma weight residual 126.40 15.98 110.42 3.00e+00 1.11e-01 1.35e+03 ... (remaining 9055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 2180 34.66 - 69.33: 90 69.33 - 103.99: 10 103.99 - 138.66: 0 138.66 - 173.32: 30 Dihedral angle restraints: 2310 sinusoidal: 1220 harmonic: 1090 Sorted by residual: dihedral pdb=" CG HIS C 13 " pdb=" ND1 HIS C 13 " pdb=" CE1 HIS C 13 " pdb=" HD2 HIS C 13 " ideal model delta harmonic sigma weight residual -180.00 -6.68 -173.32 0 5.00e+00 4.00e-02 1.20e+03 dihedral pdb=" CG HIS I 13 " pdb=" ND1 HIS I 13 " pdb=" CE1 HIS I 13 " pdb=" HD2 HIS I 13 " ideal model delta harmonic sigma weight residual -180.00 -6.68 -173.32 0 5.00e+00 4.00e-02 1.20e+03 dihedral pdb=" CG HIS A 13 " pdb=" ND1 HIS A 13 " pdb=" CE1 HIS A 13 " pdb=" HE1 HIS A 13 " ideal model delta harmonic sigma weight residual -180.00 -6.70 -173.30 0 5.00e+00 4.00e-02 1.20e+03 ... (remaining 2307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 221 0.027 - 0.054: 66 0.054 - 0.081: 20 0.081 - 0.108: 33 0.108 - 0.135: 50 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE H 31 " pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CB ILE H 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 387 not shown) Planarity restraints: 750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 13 " -0.004 2.00e-02 2.50e+03 5.59e-02 7.03e+01 pdb=" CG HIS I 13 " 0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS I 13 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS I 13 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 HIS I 13 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS I 13 " 0.065 2.00e-02 2.50e+03 pdb=" HD1 HIS I 13 " 0.090 2.00e-02 2.50e+03 pdb=" HD2 HIS I 13 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS I 13 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 13 " 0.004 2.00e-02 2.50e+03 5.58e-02 7.01e+01 pdb=" CG HIS H 13 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS H 13 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS H 13 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 HIS H 13 " -0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS H 13 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 HIS H 13 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 HIS H 13 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS H 13 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS J 13 " 0.004 2.00e-02 2.50e+03 5.58e-02 6.99e+01 pdb=" CG HIS J 13 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS J 13 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS J 13 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS J 13 " -0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS J 13 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 HIS J 13 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 HIS J 13 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 HIS J 13 " 0.026 2.00e-02 2.50e+03 ... (remaining 747 not shown) Histogram of nonbonded interaction distances: 0.69 - 1.48: 20 1.48 - 2.26: 803 2.26 - 3.04: 14642 3.04 - 3.82: 20572 3.82 - 4.60: 33806 Warning: very small nonbonded interaction distances. Nonbonded interactions: 69843 Sorted by model distance: nonbonded pdb=" CD2 HIS D 13 " pdb=" HD2 HIS D 13 " model vdw 0.694 2.240 nonbonded pdb=" CD2 HIS J 13 " pdb=" HD2 HIS J 13 " model vdw 0.695 2.240 nonbonded pdb=" CD2 HIS E 13 " pdb=" HD2 HIS E 13 " model vdw 0.695 2.240 nonbonded pdb=" CD2 HIS C 13 " pdb=" HD2 HIS C 13 " model vdw 0.695 2.240 nonbonded pdb=" CD2 HIS B 13 " pdb=" HD2 HIS B 13 " model vdw 0.696 2.240 ... (remaining 69838 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: 0.00 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' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.530 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: 0.090 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.670 Find NCS groups from input model: 0.140 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.009 0.098 2510 Z= 0.556 Angle : 0.671 5.540 3380 Z= 0.579 Chirality : 0.057 0.135 390 Planarity : 0.008 0.052 430 Dihedral : 9.518 37.061 850 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.069 0.023 HIS G 13 PHE 0.003 0.001 PHE J 19 TYR 0.003 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1492 time to fit residues: 15.4258 Evaluate side-chains 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.0030 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS C 14 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 HIS J 14 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4945 r_free = 0.4945 target = 0.253584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.187482 restraints weight = 12052.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.196313 restraints weight = 4767.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.201764 restraints weight = 2587.448| |-----------------------------------------------------------------------------| r_work (final): 0.5019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5026 r_free = 0.5026 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5024 r_free = 0.5024 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.5024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2510 Z= 0.227 Angle : 0.447 2.764 3380 Z= 0.269 Chirality : 0.058 0.153 390 Planarity : 0.002 0.006 430 Dihedral : 5.385 15.890 340 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.00 % Allowed : 12.40 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.50), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.08 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.013 0.002 PHE C 19 TYR 0.002 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.1618 time to fit residues: 10.4074 Evaluate side-chains 35 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS D 14 HIS ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS H 14 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.244264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.179861 restraints weight = 12625.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.187804 restraints weight = 5076.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.192830 restraints weight = 2851.866| |-----------------------------------------------------------------------------| r_work (final): 0.4980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2510 Z= 0.263 Angle : 0.464 3.095 3380 Z= 0.277 Chirality : 0.059 0.150 390 Planarity : 0.002 0.007 430 Dihedral : 7.008 27.536 340 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.40 % Allowed : 10.80 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.08 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 14 PHE 0.015 0.003 PHE A 19 TYR 0.003 0.001 TYR G 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 49 average time/residue: 0.1490 time to fit residues: 10.2224 Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 27 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.177957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.151333 restraints weight = 13669.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.157439 restraints weight = 5840.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.161923 restraints weight = 3437.585| |-----------------------------------------------------------------------------| r_work (final): 0.4971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2510 Z= 0.127 Angle : 0.415 2.482 3380 Z= 0.244 Chirality : 0.060 0.149 390 Planarity : 0.001 0.005 430 Dihedral : 5.898 20.455 340 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.80 % Allowed : 15.20 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.21 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 14 PHE 0.005 0.001 PHE C 19 TYR 0.004 0.001 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.586 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.1613 time to fit residues: 8.3251 Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 0.0980 chunk 25 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.168255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.142586 restraints weight = 13266.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.148121 restraints weight = 5448.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.152308 restraints weight = 3197.328| |-----------------------------------------------------------------------------| r_work (final): 0.4853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2510 Z= 0.215 Angle : 0.423 2.676 3380 Z= 0.251 Chirality : 0.058 0.144 390 Planarity : 0.002 0.005 430 Dihedral : 6.425 25.232 340 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.20 % Allowed : 16.80 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.24 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 14 PHE 0.010 0.002 PHE C 19 TYR 0.004 0.001 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 1.169 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 37 average time/residue: 0.2143 time to fit residues: 12.0334 Evaluate side-chains 34 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.162691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.137172 restraints weight = 13196.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.142332 restraints weight = 5633.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.146318 restraints weight = 3362.117| |-----------------------------------------------------------------------------| r_work (final): 0.4785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2510 Z= 0.365 Angle : 0.495 3.447 3380 Z= 0.295 Chirality : 0.059 0.151 390 Planarity : 0.002 0.009 430 Dihedral : 8.085 36.499 340 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.20 % Allowed : 15.60 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.41 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 14 PHE 0.015 0.003 PHE C 19 TYR 0.005 0.002 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.503 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 41 average time/residue: 0.1599 time to fit residues: 9.7004 Evaluate side-chains 38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.170364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.145054 restraints weight = 12817.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.150712 restraints weight = 5074.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.154962 restraints weight = 2893.934| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2510 Z= 0.137 Angle : 0.416 5.546 3380 Z= 0.237 Chirality : 0.059 0.146 390 Planarity : 0.001 0.010 430 Dihedral : 6.474 25.514 340 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.60 % Allowed : 18.40 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 13 PHE 0.005 0.001 PHE C 19 TYR 0.004 0.001 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.410 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.1380 time to fit residues: 8.4577 Evaluate side-chains 33 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.164076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.139199 restraints weight = 13430.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.144685 restraints weight = 5470.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.148279 restraints weight = 3128.532| |-----------------------------------------------------------------------------| r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2510 Z= 0.289 Angle : 0.452 3.130 3380 Z= 0.266 Chirality : 0.058 0.157 390 Planarity : 0.002 0.008 430 Dihedral : 7.256 31.035 340 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.80 % Allowed : 19.20 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 14 PHE 0.012 0.002 PHE A 19 TYR 0.004 0.001 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.378 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.1308 time to fit residues: 6.5794 Evaluate side-chains 34 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.175504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.149478 restraints weight = 12637.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.155369 restraints weight = 5036.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.159721 restraints weight = 2835.474| |-----------------------------------------------------------------------------| r_work (final): 0.4926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2510 Z= 0.113 Angle : 0.398 3.716 3380 Z= 0.227 Chirality : 0.059 0.140 390 Planarity : 0.001 0.005 430 Dihedral : 5.722 19.694 340 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.60 % Allowed : 21.20 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.46), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 13 PHE 0.004 0.001 PHE C 19 TYR 0.002 0.000 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.388 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 35 average time/residue: 0.1356 time to fit residues: 6.9268 Evaluate side-chains 30 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.168048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.142953 restraints weight = 13579.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.148590 restraints weight = 5506.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.152906 restraints weight = 3157.695| |-----------------------------------------------------------------------------| r_work (final): 0.4909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2510 Z= 0.260 Angle : 0.432 2.781 3380 Z= 0.254 Chirality : 0.057 0.149 390 Planarity : 0.002 0.006 430 Dihedral : 6.588 26.816 340 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 2.00 % Allowed : 20.40 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.47), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 14 PHE 0.011 0.002 PHE C 19 TYR 0.004 0.001 TYR D 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.449 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 34 average time/residue: 0.1460 time to fit residues: 7.3911 Evaluate side-chains 32 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.172378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.146580 restraints weight = 13091.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.152318 restraints weight = 5163.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.156476 restraints weight = 2911.260| |-----------------------------------------------------------------------------| r_work (final): 0.4957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2510 Z= 0.154 Angle : 0.400 2.717 3380 Z= 0.230 Chirality : 0.058 0.142 390 Planarity : 0.001 0.005 430 Dihedral : 5.936 22.871 340 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.40 % Allowed : 22.40 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.46), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.006 0.001 PHE C 19 TYR 0.003 0.001 TYR J 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.28 seconds wall clock time: 61 minutes 1.61 seconds (3661.61 seconds total)