Starting phenix.real_space_refine on Fri May 9 14:00:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gz6_51726/05_2025/9gz6_51726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gz6_51726/05_2025/9gz6_51726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gz6_51726/05_2025/9gz6_51726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gz6_51726/05_2025/9gz6_51726.map" model { file = "/net/cci-nas-00/data/ceres_data/9gz6_51726/05_2025/9gz6_51726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gz6_51726/05_2025/9gz6_51726.cif" } resolution = 3.3 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= 0.001 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 1440 2.51 5 N 408 2.21 5 O 468 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-5687/modules/chem_data/mon_lib" Total number of atoms: 2316 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 192 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} 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: 1.24, per 1000 atoms: 0.54 Number of scatterers: 2316 At special positions: 0 Unit cell: (58.855, 69.285, 46.935, 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 468 8.00 N 408 7.00 C 1440 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 281.9 milliseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 57.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 22 removed outlier: 6.605A pdb=" N ALA A 13 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N LEU C 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS C 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 17 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER C 20 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SER A 19 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN C 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN A 21 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA C 13 " --> pdb=" O ASN E 14 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU E 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE C 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N HIS E 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL C 17 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER E 20 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER C 19 " --> pdb=" O SER E 20 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN E 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASN C 21 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 13 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU G 16 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS G 18 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL E 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER G 20 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER E 19 " --> pdb=" O SER G 20 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN G 22 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN E 21 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA G 13 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N LEU I 16 " --> pdb=" O ALA G 13 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE G 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS I 18 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL G 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER I 20 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER G 19 " --> pdb=" O SER I 20 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN I 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN G 21 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER K 20 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN I 21 " --> pdb=" O SER K 20 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASN K 22 " --> pdb=" O ASN I 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.614A pdb=" N ILE A 26 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SER C 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER A 28 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASN C 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 26 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER E 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 28 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASN E 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE G 26 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER I 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER G 28 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASN I 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR G 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE I 26 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N SER K 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER I 28 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASN K 31 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR I 30 " --> pdb=" O ASN K 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 22 removed outlier: 6.546A pdb=" N ALA B 13 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU D 16 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE B 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS D 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B 17 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N SER D 20 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER B 19 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN D 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN B 21 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN F 22 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 13 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU H 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE F 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS H 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL F 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER H 20 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER F 19 " --> pdb=" O SER H 20 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN H 22 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN F 21 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA H 13 " --> pdb=" O ASN J 14 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU J 16 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE H 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N HIS J 18 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL H 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N SER J 20 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER H 19 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASN J 22 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASN H 21 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER L 20 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN J 21 " --> pdb=" O SER L 20 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN L 22 " --> pdb=" O ASN J 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 31 removed outlier: 3.510A pdb=" N SER D 29 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE H 26 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N SER J 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER H 28 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASN J 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR H 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE J 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER L 29 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER J 28 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN L 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR J 30 " --> pdb=" O ASN L 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AA7, first strand: chain 'J' and resid 35 through 36 47 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.72 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: 372 1.29 - 1.35: 384 1.35 - 1.41: 264 1.41 - 1.48: 396 1.48 - 1.54: 924 Bond restraints: 2340 Sorted by residual: bond pdb=" N SER F 34 " pdb=" CA SER F 34 " ideal model delta sigma weight residual 1.455 1.462 -0.006 1.33e-02 5.65e+03 2.30e-01 bond pdb=" N SER C 34 " pdb=" CA SER C 34 " ideal model delta sigma weight residual 1.455 1.462 -0.006 1.33e-02 5.65e+03 2.23e-01 bond pdb=" N SER B 34 " pdb=" CA SER B 34 " ideal model delta sigma weight residual 1.455 1.461 -0.006 1.33e-02 5.65e+03 2.10e-01 bond pdb=" N SER I 34 " pdb=" CA SER I 34 " ideal model delta sigma weight residual 1.455 1.461 -0.006 1.33e-02 5.65e+03 2.07e-01 bond pdb=" N SER H 34 " pdb=" CA SER H 34 " ideal model delta sigma weight residual 1.455 1.461 -0.006 1.33e-02 5.65e+03 1.96e-01 ... (remaining 2335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 2859 1.30 - 2.61: 238 2.61 - 3.91: 35 3.91 - 5.22: 36 5.22 - 6.52: 12 Bond angle restraints: 3180 Sorted by residual: angle pdb=" N ASN D 22 " pdb=" CA ASN D 22 " pdb=" C ASN D 22 " ideal model delta sigma weight residual 108.73 112.94 -4.21 1.63e+00 3.76e-01 6.66e+00 angle pdb=" N ASN C 22 " pdb=" CA ASN C 22 " pdb=" C ASN C 22 " ideal model delta sigma weight residual 108.73 112.92 -4.19 1.63e+00 3.76e-01 6.62e+00 angle pdb=" N ASN A 22 " pdb=" CA ASN A 22 " pdb=" C ASN A 22 " ideal model delta sigma weight residual 108.73 112.92 -4.19 1.63e+00 3.76e-01 6.59e+00 angle pdb=" N ASN J 22 " pdb=" CA ASN J 22 " pdb=" C ASN J 22 " ideal model delta sigma weight residual 108.73 112.91 -4.18 1.63e+00 3.76e-01 6.56e+00 angle pdb=" N ASN B 22 " pdb=" CA ASN B 22 " pdb=" C ASN B 22 " ideal model delta sigma weight residual 108.73 112.90 -4.17 1.63e+00 3.76e-01 6.53e+00 ... (remaining 3175 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 7.46: 1044 7.46 - 14.91: 168 14.91 - 22.36: 52 22.36 - 29.81: 32 29.81 - 37.26: 12 Dihedral angle restraints: 1308 sinusoidal: 420 harmonic: 888 Sorted by residual: dihedral pdb=" N ASN J 21 " pdb=" CA ASN J 21 " pdb=" CB ASN J 21 " pdb=" CG ASN J 21 " ideal model delta sinusoidal sigma weight residual -60.00 -89.48 29.48 3 1.50e+01 4.44e-03 4.61e+00 dihedral pdb=" N ASN E 21 " pdb=" CA ASN E 21 " pdb=" CB ASN E 21 " pdb=" CG ASN E 21 " ideal model delta sinusoidal sigma weight residual -60.00 -89.48 29.48 3 1.50e+01 4.44e-03 4.61e+00 dihedral pdb=" N ASN I 21 " pdb=" CA ASN I 21 " pdb=" CB ASN I 21 " pdb=" CG ASN I 21 " ideal model delta sinusoidal sigma weight residual -60.00 -89.47 29.47 3 1.50e+01 4.44e-03 4.61e+00 ... (remaining 1305 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.027: 156 0.027 - 0.051: 151 0.051 - 0.076: 65 0.076 - 0.100: 0 0.100 - 0.125: 12 Chirality restraints: 384 Sorted by residual: chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE E 26 " pdb=" N ILE E 26 " pdb=" C ILE E 26 " pdb=" CB ILE E 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE H 26 " pdb=" N ILE H 26 " pdb=" C ILE H 26 " pdb=" CB ILE H 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 381 not shown) Planarity restraints: 408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 23 " -0.001 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE L 23 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE L 23 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE L 23 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE L 23 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE L 23 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE L 23 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 23 " -0.001 2.00e-02 2.50e+03 1.17e-02 2.39e+00 pdb=" CG PHE D 23 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE D 23 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE D 23 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 23 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE D 23 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 23 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 23 " -0.001 2.00e-02 2.50e+03 1.17e-02 2.38e+00 pdb=" CG PHE J 23 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE J 23 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE J 23 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE J 23 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE J 23 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE J 23 " -0.001 2.00e-02 2.50e+03 ... (remaining 405 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 412 2.79 - 3.32: 1963 3.32 - 3.84: 3778 3.84 - 4.37: 4360 4.37 - 4.90: 7380 Nonbonded interactions: 17893 Sorted by model distance: nonbonded pdb=" O SER H 34 " pdb=" O GLY J 33 " model vdw 2.259 3.040 nonbonded pdb=" O SER B 34 " pdb=" O GLY D 33 " model vdw 2.412 3.040 nonbonded pdb=" O SER E 34 " pdb=" O GLY G 33 " model vdw 2.424 3.040 nonbonded pdb=" N NH2 H 38 " pdb=" O TYR J 37 " model vdw 2.434 3.120 nonbonded pdb=" O SER A 34 " pdb=" O GLY C 33 " model vdw 2.466 3.040 ... (remaining 17888 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: 1.110 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.090 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 0.103 2352 Z= 0.743 Angle : 0.956 6.523 3180 Z= 0.510 Chirality : 0.042 0.125 384 Planarity : 0.003 0.012 408 Dihedral : 10.538 37.257 732 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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: -2.82 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 18 PHE 0.020 0.005 PHE L 23 TYR 0.005 0.002 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.27642 ( 47) hydrogen bonds : angle 8.77112 ( 141) covalent geometry : bond 0.00290 ( 2340) covalent geometry : angle 0.95557 ( 3180) Misc. bond : bond 0.10202 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.236 Fit side-chains REVERT: C 14 ASN cc_start: 0.7932 (t0) cc_final: 0.7632 (t0) REVERT: D 14 ASN cc_start: 0.7937 (t0) cc_final: 0.7594 (t0) REVERT: F 14 ASN cc_start: 0.7743 (t0) cc_final: 0.7542 (t0) REVERT: G 22 ASN cc_start: 0.8492 (t0) cc_final: 0.8150 (t0) REVERT: L 14 ASN cc_start: 0.7940 (t0) cc_final: 0.7685 (t0) REVERT: L 32 VAL cc_start: 0.8716 (t) cc_final: 0.8429 (p) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0598 time to fit residues: 6.9132 Evaluate side-chains 66 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** 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 = 0.4121 r_free = 0.4121 target = 0.140347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.123834 restraints weight = 3730.778| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.16 r_work: 0.3859 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2352 Z= 0.194 Angle : 0.642 5.007 3180 Z= 0.333 Chirality : 0.041 0.134 384 Planarity : 0.002 0.007 408 Dihedral : 5.468 13.400 312 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 20.83 % Favored : 77.27 % 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: -3.54 (0.23), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.18), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 18 PHE 0.013 0.002 PHE K 15 TYR 0.006 0.001 TYR K 37 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 47) hydrogen bonds : angle 6.18577 ( 141) covalent geometry : bond 0.00414 ( 2340) covalent geometry : angle 0.64155 ( 3180) Misc. bond : bond 0.00138 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.263 Fit side-chains REVERT: D 14 ASN cc_start: 0.7731 (t0) cc_final: 0.7370 (t0) REVERT: L 32 VAL cc_start: 0.8871 (t) cc_final: 0.8611 (p) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.0583 time to fit residues: 5.6464 Evaluate side-chains 63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain I residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN ** E 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.137084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.120376 restraints weight = 4086.769| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.36 r_work: 0.3795 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 2352 Z= 0.226 Angle : 0.588 4.397 3180 Z= 0.320 Chirality : 0.041 0.135 384 Planarity : 0.002 0.008 408 Dihedral : 5.789 14.111 312 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 4.17 % Allowed : 16.29 % Favored : 79.55 % 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: -4.16 (0.23), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.17), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 18 PHE 0.013 0.003 PHE K 15 TYR 0.005 0.001 TYR B 37 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 47) hydrogen bonds : angle 5.76256 ( 141) covalent geometry : bond 0.00478 ( 2340) covalent geometry : angle 0.58809 ( 3180) Misc. bond : bond 0.00054 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.247 Fit side-chains REVERT: C 22 ASN cc_start: 0.8645 (t0) cc_final: 0.8129 (t0) REVERT: D 14 ASN cc_start: 0.7810 (t0) cc_final: 0.7428 (t0) REVERT: F 22 ASN cc_start: 0.8707 (t0) cc_final: 0.8500 (t0) REVERT: F 32 VAL cc_start: 0.8790 (t) cc_final: 0.8519 (p) REVERT: K 32 VAL cc_start: 0.8918 (t) cc_final: 0.8696 (p) REVERT: L 32 VAL cc_start: 0.8978 (t) cc_final: 0.8746 (p) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.0567 time to fit residues: 4.9083 Evaluate side-chains 65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain L residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.118830 restraints weight = 4332.504| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.47 r_work: 0.3763 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2352 Z= 0.259 Angle : 0.585 4.160 3180 Z= 0.325 Chirality : 0.042 0.133 384 Planarity : 0.002 0.009 408 Dihedral : 5.928 16.681 312 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.79 % Allowed : 18.56 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.24), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.18), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 18 PHE 0.013 0.003 PHE J 15 TYR 0.006 0.001 TYR B 37 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 47) hydrogen bonds : angle 5.51621 ( 141) covalent geometry : bond 0.00547 ( 2340) covalent geometry : angle 0.58533 ( 3180) Misc. bond : bond 0.00142 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.272 Fit side-chains REVERT: C 32 VAL cc_start: 0.8805 (t) cc_final: 0.8536 (p) REVERT: D 14 ASN cc_start: 0.7816 (t0) cc_final: 0.7449 (t0) REVERT: F 22 ASN cc_start: 0.8761 (t0) cc_final: 0.8503 (t0) REVERT: F 32 VAL cc_start: 0.8661 (t) cc_final: 0.8436 (p) REVERT: G 32 VAL cc_start: 0.8806 (t) cc_final: 0.8547 (p) REVERT: J 32 VAL cc_start: 0.8679 (t) cc_final: 0.8447 (p) REVERT: K 32 VAL cc_start: 0.8858 (t) cc_final: 0.8658 (p) REVERT: L 32 VAL cc_start: 0.8928 (t) cc_final: 0.8614 (p) outliers start: 10 outliers final: 10 residues processed: 58 average time/residue: 0.0598 time to fit residues: 4.9934 Evaluate side-chains 61 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 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 22 ASN C 22 ASN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.137086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.118858 restraints weight = 5090.289| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.68 r_work: 0.3780 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 2352 Z= 0.176 Angle : 0.508 3.820 3180 Z= 0.282 Chirality : 0.040 0.130 384 Planarity : 0.002 0.007 408 Dihedral : 5.566 15.046 312 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.41 % Allowed : 18.56 % Favored : 78.03 % 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 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.010 0.002 PHE J 15 TYR 0.004 0.001 TYR B 37 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 47) hydrogen bonds : angle 5.25212 ( 141) covalent geometry : bond 0.00367 ( 2340) covalent geometry : angle 0.50831 ( 3180) Misc. bond : bond 0.00052 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.275 Fit side-chains REVERT: C 32 VAL cc_start: 0.8841 (t) cc_final: 0.8585 (p) REVERT: D 14 ASN cc_start: 0.7780 (t0) cc_final: 0.7466 (t0) REVERT: J 32 VAL cc_start: 0.8654 (t) cc_final: 0.8435 (p) REVERT: L 32 VAL cc_start: 0.8914 (t) cc_final: 0.8628 (p) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.0589 time to fit residues: 4.5783 Evaluate side-chains 53 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain K residue 31 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 ASN F 22 ASN ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN L 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.137433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119019 restraints weight = 4647.944| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.59 r_work: 0.3807 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2352 Z= 0.145 Angle : 0.483 3.620 3180 Z= 0.269 Chirality : 0.039 0.126 384 Planarity : 0.002 0.008 408 Dihedral : 5.326 14.764 312 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.65 % Allowed : 21.97 % Favored : 75.38 % 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: -4.27 (0.26), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.20), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 18 PHE 0.008 0.002 PHE J 15 TYR 0.003 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 47) hydrogen bonds : angle 4.91085 ( 141) covalent geometry : bond 0.00300 ( 2340) covalent geometry : angle 0.48292 ( 3180) Misc. bond : bond 0.00038 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.255 Fit side-chains REVERT: B 32 VAL cc_start: 0.8513 (t) cc_final: 0.8235 (p) REVERT: D 14 ASN cc_start: 0.7734 (t0) cc_final: 0.7440 (t0) REVERT: D 31 ASN cc_start: 0.8164 (m110) cc_final: 0.7860 (m-40) REVERT: E 29 SER cc_start: 0.8634 (p) cc_final: 0.8398 (p) REVERT: G 31 ASN cc_start: 0.7759 (m110) cc_final: 0.7447 (m-40) REVERT: J 32 VAL cc_start: 0.8648 (t) cc_final: 0.8436 (p) REVERT: K 22 ASN cc_start: 0.8224 (t0) cc_final: 0.7962 (t0) REVERT: L 32 VAL cc_start: 0.8878 (t) cc_final: 0.8555 (m) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.0589 time to fit residues: 4.1231 Evaluate side-chains 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain I residue 31 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.134921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116530 restraints weight = 4789.686| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.71 r_work: 0.3757 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2352 Z= 0.220 Angle : 0.524 4.093 3180 Z= 0.295 Chirality : 0.040 0.130 384 Planarity : 0.002 0.008 408 Dihedral : 5.512 16.373 312 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.17 % Allowed : 20.08 % Favored : 75.76 % 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: -4.30 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.011 0.002 PHE J 15 TYR 0.004 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 47) hydrogen bonds : angle 4.87701 ( 141) covalent geometry : bond 0.00465 ( 2340) covalent geometry : angle 0.52402 ( 3180) Misc. bond : bond 0.00059 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.246 Fit side-chains REVERT: B 32 VAL cc_start: 0.8516 (t) cc_final: 0.8223 (p) REVERT: D 31 ASN cc_start: 0.8128 (m110) cc_final: 0.7843 (m-40) REVERT: E 29 SER cc_start: 0.8672 (p) cc_final: 0.8444 (p) REVERT: G 31 ASN cc_start: 0.7871 (m110) cc_final: 0.7491 (m-40) REVERT: H 31 ASN cc_start: 0.7782 (m110) cc_final: 0.7543 (m-40) REVERT: H 32 VAL cc_start: 0.8695 (t) cc_final: 0.8329 (m) REVERT: L 32 VAL cc_start: 0.8878 (t) cc_final: 0.8612 (m) outliers start: 11 outliers final: 9 residues processed: 45 average time/residue: 0.0570 time to fit residues: 3.7610 Evaluate side-chains 50 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.132903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.115012 restraints weight = 4644.623| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.59 r_work: 0.3761 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2352 Z= 0.307 Angle : 0.592 4.481 3180 Z= 0.335 Chirality : 0.041 0.132 384 Planarity : 0.003 0.010 408 Dihedral : 5.830 17.969 312 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.30 % Allowed : 19.32 % Favored : 75.38 % 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: -4.50 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 18 PHE 0.016 0.003 PHE J 15 TYR 0.006 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 47) hydrogen bonds : angle 5.02733 ( 141) covalent geometry : bond 0.00653 ( 2340) covalent geometry : angle 0.59198 ( 3180) Misc. bond : bond 0.00090 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.262 Fit side-chains REVERT: C 22 ASN cc_start: 0.8798 (t0) cc_final: 0.8219 (t0) REVERT: E 29 SER cc_start: 0.8736 (p) cc_final: 0.8483 (p) REVERT: G 31 ASN cc_start: 0.7880 (m110) cc_final: 0.7654 (m-40) REVERT: H 31 ASN cc_start: 0.7869 (m110) cc_final: 0.7543 (m-40) REVERT: H 32 VAL cc_start: 0.8595 (t) cc_final: 0.8244 (m) REVERT: L 32 VAL cc_start: 0.8854 (t) cc_final: 0.8598 (m) outliers start: 14 outliers final: 13 residues processed: 42 average time/residue: 0.0580 time to fit residues: 3.6690 Evaluate side-chains 51 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain K residue 31 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.116901 restraints weight = 4927.329| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 3.77 r_work: 0.3778 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2352 Z= 0.188 Angle : 0.505 3.864 3180 Z= 0.285 Chirality : 0.039 0.127 384 Planarity : 0.002 0.008 408 Dihedral : 5.407 17.172 312 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.17 % Allowed : 20.83 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.010 0.002 PHE D 15 TYR 0.004 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 47) hydrogen bonds : angle 4.88239 ( 141) covalent geometry : bond 0.00395 ( 2340) covalent geometry : angle 0.50478 ( 3180) Misc. bond : bond 0.00061 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.266 Fit side-chains REVERT: B 32 VAL cc_start: 0.8446 (t) cc_final: 0.8184 (p) REVERT: C 22 ASN cc_start: 0.8759 (t0) cc_final: 0.8174 (t0) REVERT: E 29 SER cc_start: 0.8715 (p) cc_final: 0.8511 (p) REVERT: G 31 ASN cc_start: 0.7855 (m110) cc_final: 0.7563 (m-40) REVERT: H 31 ASN cc_start: 0.7695 (m110) cc_final: 0.7367 (m-40) REVERT: H 32 VAL cc_start: 0.8581 (t) cc_final: 0.8212 (m) REVERT: L 32 VAL cc_start: 0.8841 (t) cc_final: 0.8582 (m) outliers start: 11 outliers final: 10 residues processed: 47 average time/residue: 0.0591 time to fit residues: 4.0458 Evaluate side-chains 51 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain K residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.132323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114549 restraints weight = 4447.971| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.50 r_work: 0.3754 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 2352 Z= 0.365 Angle : 0.636 4.655 3180 Z= 0.360 Chirality : 0.042 0.131 384 Planarity : 0.003 0.010 408 Dihedral : 6.024 18.622 312 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.92 % Allowed : 18.94 % Favored : 76.14 % 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: -4.73 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS L 18 PHE 0.018 0.004 PHE I 15 TYR 0.006 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 47) hydrogen bonds : angle 5.29299 ( 141) covalent geometry : bond 0.00776 ( 2340) covalent geometry : angle 0.63550 ( 3180) Misc. bond : bond 0.00110 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.265 Fit side-chains REVERT: C 22 ASN cc_start: 0.8798 (t0) cc_final: 0.8183 (t0) REVERT: C 29 SER cc_start: 0.9000 (p) cc_final: 0.8775 (p) REVERT: E 29 SER cc_start: 0.8838 (p) cc_final: 0.8609 (p) REVERT: G 31 ASN cc_start: 0.7879 (m110) cc_final: 0.7589 (m-40) REVERT: H 31 ASN cc_start: 0.7720 (m110) cc_final: 0.7399 (m-40) REVERT: K 29 SER cc_start: 0.9020 (p) cc_final: 0.8786 (p) REVERT: L 32 VAL cc_start: 0.8835 (t) cc_final: 0.8569 (m) outliers start: 13 outliers final: 13 residues processed: 45 average time/residue: 0.0579 time to fit residues: 3.8727 Evaluate side-chains 52 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 31 ASN Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain L residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.115725 restraints weight = 4645.527| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.64 r_work: 0.3777 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2352 Z= 0.213 Angle : 0.526 4.044 3180 Z= 0.296 Chirality : 0.039 0.125 384 Planarity : 0.002 0.007 408 Dihedral : 5.559 17.865 312 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.79 % Allowed : 21.21 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 18 PHE 0.012 0.002 PHE J 15 TYR 0.004 0.001 TYR F 37 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 47) hydrogen bonds : angle 5.13310 ( 141) covalent geometry : bond 0.00447 ( 2340) covalent geometry : angle 0.52551 ( 3180) Misc. bond : bond 0.00061 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1229.77 seconds wall clock time: 22 minutes 27.25 seconds (1347.25 seconds total)