Starting phenix.real_space_refine on Mon Sep 23 19:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/09_2024/7q66_13853.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/09_2024/7q66_13853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/09_2024/7q66_13853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/09_2024/7q66_13853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/09_2024/7q66_13853.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/09_2024/7q66_13853.cif" } resolution = 2.79 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= 0.001 sd= 0.009 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 2959 2.51 5 N 814 2.21 5 O 1034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4807 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, D, F, H, J, L, N, P, R, T, V Time building chain proxies: 1.73, per 1000 atoms: 0.36 Number of scatterers: 4807 At special positions: 0 Unit cell: (66.15, 61.95, 72.45, 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 1034 8.00 N 814 7.00 C 2959 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=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 604.6 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 53.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.095A pdb=" N ALA A 88 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU C 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR A 90 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 88 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU E 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR C 90 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA E 88 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU G 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR E 90 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA G 88 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU I 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR G 90 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA I 88 " --> pdb=" O ASN K 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU K 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR I 90 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA K 88 " --> pdb=" O ASN M 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU M 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR K 90 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 88 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU O 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR M 90 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA O 88 " --> pdb=" O ASN Q 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU Q 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR O 90 " --> pdb=" O LEU Q 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA Q 88 " --> pdb=" O ASN S 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU S 91 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR Q 90 " --> pdb=" O LEU S 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA S 88 " --> pdb=" O ASN U 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU U 91 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR S 90 " --> pdb=" O LEU U 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.382A pdb=" N ALA A 95 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA C 95 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA E 95 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA G 95 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA I 95 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA K 95 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA M 95 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA O 95 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA Q 95 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA S 95 " --> pdb=" O SER U 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 112 removed outlier: 6.882A pdb=" N ASN A 106 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE C 109 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA A 108 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN C 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 110 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN C 106 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE E 109 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA C 108 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN E 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA C 110 " --> pdb=" O GLN E 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 106 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE G 109 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA E 108 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN G 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA E 110 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN G 106 " --> pdb=" O ASN I 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE I 109 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA G 108 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN I 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA G 110 " --> pdb=" O GLN I 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN I 106 " --> pdb=" O ASN K 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE K 109 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA I 108 " --> pdb=" O PHE K 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN K 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA I 110 " --> pdb=" O GLN K 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN K 106 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE M 109 " --> pdb=" O ASN K 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA K 108 " --> pdb=" O PHE M 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN M 111 " --> pdb=" O ALA K 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA K 110 " --> pdb=" O GLN M 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN M 106 " --> pdb=" O ASN O 107 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE O 109 " --> pdb=" O ASN M 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA M 108 " --> pdb=" O PHE O 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN O 111 " --> pdb=" O ALA M 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA M 110 " --> pdb=" O GLN O 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN O 106 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE Q 109 " --> pdb=" O ASN O 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA O 108 " --> pdb=" O PHE Q 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN Q 111 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA O 110 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN Q 106 " --> pdb=" O ASN S 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE S 109 " --> pdb=" O ASN Q 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA Q 108 " --> pdb=" O PHE S 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN S 111 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA Q 110 " --> pdb=" O GLN S 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN S 106 " --> pdb=" O ASN U 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE U 109 " --> pdb=" O ASN S 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA S 108 " --> pdb=" O PHE U 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN U 111 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA S 110 " --> pdb=" O GLN U 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 120 removed outlier: 6.517A pdb=" N THR A 115 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY C 118 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 117 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE C 120 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN A 119 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR C 115 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY E 118 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE C 117 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE E 120 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN C 119 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR E 115 " --> pdb=" O GLY G 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY G 118 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE E 117 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE G 120 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN E 119 " --> pdb=" O PHE G 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR G 115 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY I 118 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE G 117 " --> pdb=" O GLY I 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE I 120 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN G 119 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR I 115 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY K 118 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE I 117 " --> pdb=" O GLY K 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE K 120 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN I 119 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR K 115 " --> pdb=" O GLY M 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY M 118 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE K 117 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE M 120 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN K 119 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR M 115 " --> pdb=" O GLY O 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY O 118 " --> pdb=" O THR M 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE M 117 " --> pdb=" O GLY O 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE O 120 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN M 119 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR O 115 " --> pdb=" O GLY Q 116 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLY Q 118 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE O 117 " --> pdb=" O GLY Q 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE Q 120 " --> pdb=" O PHE O 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN O 119 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR Q 115 " --> pdb=" O GLY S 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY S 118 " --> pdb=" O THR Q 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE Q 117 " --> pdb=" O GLY S 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE S 120 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN Q 119 " --> pdb=" O PHE S 120 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR S 115 " --> pdb=" O GLY U 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY U 118 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE S 117 " --> pdb=" O GLY U 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE U 120 " --> pdb=" O PHE S 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN S 119 " --> pdb=" O PHE U 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 108 160 hydrogen bonds defined for protein. 480 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: 1.34 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 803 1.27 - 1.34: 803 1.34 - 1.41: 594 1.41 - 1.47: 979 1.47 - 1.54: 1705 Bond restraints: 4884 Sorted by residual: bond pdb=" CB THR A 90 " pdb=" CG2 THR A 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.57e+01 bond pdb=" CB THR C 90 " pdb=" CG2 THR C 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR K 90 " pdb=" CG2 THR K 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR O 90 " pdb=" CG2 THR O 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR M 90 " pdb=" CG2 THR M 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 ... (remaining 4879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 5817 1.89 - 3.78: 563 3.78 - 5.67: 176 5.67 - 7.56: 33 7.56 - 9.45: 22 Bond angle restraints: 6611 Sorted by residual: angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" C LYS A 113 " ideal model delta sigma weight residual 111.53 119.09 -7.56 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS G 113 " pdb=" CA LYS G 113 " pdb=" C LYS G 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS U 113 " pdb=" CA LYS U 113 " pdb=" C LYS U 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" C LYS K 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS O 113 " pdb=" CA LYS O 113 " pdb=" C LYS O 113 " ideal model delta sigma weight residual 111.53 119.07 -7.54 2.18e+00 2.10e-01 1.20e+01 ... (remaining 6606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.71: 2376 12.71 - 25.42: 209 25.42 - 38.13: 66 38.13 - 50.84: 11 50.84 - 63.55: 11 Dihedral angle restraints: 2673 sinusoidal: 847 harmonic: 1826 Sorted by residual: dihedral pdb=" C LYS K 113 " pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" CB LYS K 113 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" C LYS M 113 " pdb=" N LYS M 113 " pdb=" CA LYS M 113 " pdb=" CB LYS M 113 " ideal model delta harmonic sigma weight residual -122.60 -131.54 8.94 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" C LYS I 113 " pdb=" N LYS I 113 " pdb=" CA LYS I 113 " pdb=" CB LYS I 113 " ideal model delta harmonic sigma weight residual -122.60 -131.54 8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 2670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 638 0.096 - 0.191: 66 0.191 - 0.287: 33 0.287 - 0.383: 11 0.383 - 0.478: 22 Chirality restraints: 770 Sorted by residual: chirality pdb=" CG LEU B 101 " pdb=" CB LEU B 101 " pdb=" CD1 LEU B 101 " pdb=" CD2 LEU B 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CG LEU T 101 " pdb=" CB LEU T 101 " pdb=" CD1 LEU T 101 " pdb=" CD2 LEU T 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CG LEU F 101 " pdb=" CB LEU F 101 " pdb=" CD1 LEU F 101 " pdb=" CD2 LEU F 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 767 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA Q 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA Q 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN Q 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA U 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA U 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN U 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA S 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA S 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA S 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN S 111 " 0.014 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1632 2.80 - 3.33: 4132 3.33 - 3.85: 9177 3.85 - 4.38: 11100 4.38 - 4.90: 21252 Nonbonded interactions: 47293 Sorted by model distance: nonbonded pdb=" ND2 ASN A 106 " pdb=" OG SER B 103 " model vdw 2.277 3.120 nonbonded pdb=" ND2 ASN G 106 " pdb=" OG SER H 103 " model vdw 2.277 3.120 nonbonded pdb=" ND2 ASN S 106 " pdb=" OG SER T 103 " model vdw 2.278 3.120 nonbonded pdb=" ND2 ASN O 106 " pdb=" OG SER P 103 " model vdw 2.278 3.120 nonbonded pdb=" ND2 ASN U 106 " pdb=" OG SER V 103 " model vdw 2.278 3.120 ... (remaining 47288 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.021 0.167 4884 Z= 1.342 Angle : 1.424 9.452 6611 Z= 0.782 Chirality : 0.115 0.478 770 Planarity : 0.007 0.024 880 Dihedral : 12.578 63.547 1507 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.52 % Allowed : 4.35 % Favored : 89.13 % 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: -4.18 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.006 PHE S 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 0.509 Fit side-chains REVERT: H 105 GLN cc_start: 0.8627 (tt0) cc_final: 0.8409 (tt0) REVERT: K 107 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8224 (p0) REVERT: M 105 GLN cc_start: 0.8601 (tm130) cc_final: 0.8332 (tm-30) REVERT: O 107 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8261 (p0) REVERT: P 105 GLN cc_start: 0.8903 (tt0) cc_final: 0.8616 (tt0) REVERT: R 87 THR cc_start: 0.8477 (p) cc_final: 0.8115 (t) REVERT: S 105 GLN cc_start: 0.8773 (tm130) cc_final: 0.8525 (tm130) outliers start: 33 outliers final: 6 residues processed: 269 average time/residue: 0.4797 time to fit residues: 140.3270 Evaluate side-chains 184 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain R residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 105 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN H 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN ** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4884 Z= 0.267 Angle : 0.737 9.884 6611 Z= 0.349 Chirality : 0.047 0.219 770 Planarity : 0.003 0.019 880 Dihedral : 6.463 46.453 676 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 17.39 % Allowed : 16.60 % Favored : 66.01 % 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 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.12), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE G 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 208 time to evaluate : 0.563 Fit side-chains REVERT: A 94 THR cc_start: 0.8945 (t) cc_final: 0.8740 (m) REVERT: C 106 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7854 (p0) REVERT: E 112 ASN cc_start: 0.8865 (t0) cc_final: 0.8632 (t0) REVERT: H 105 GLN cc_start: 0.8536 (tt0) cc_final: 0.8329 (tt0) REVERT: I 107 ASN cc_start: 0.8267 (p0) cc_final: 0.8045 (p0) REVERT: M 106 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.7949 (p0) REVERT: M 107 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8273 (p0) REVERT: N 89 ASN cc_start: 0.8714 (m-40) cc_final: 0.8375 (m110) REVERT: P 105 GLN cc_start: 0.8816 (tt0) cc_final: 0.8410 (tt0) REVERT: S 105 GLN cc_start: 0.8792 (tm130) cc_final: 0.8450 (tm-30) outliers start: 88 outliers final: 51 residues processed: 248 average time/residue: 0.3543 time to fit residues: 98.0842 Evaluate side-chains 229 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 175 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 105 GLN D 89 ASN F 89 ASN F 105 GLN G 112 ASN H 89 ASN H 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 89 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN R 89 ASN R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 GLN U 106 ASN V 105 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4884 Z= 0.227 Angle : 0.676 9.217 6611 Z= 0.308 Chirality : 0.044 0.198 770 Planarity : 0.002 0.014 880 Dihedral : 5.425 26.655 670 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 13.64 % Allowed : 24.70 % Favored : 61.66 % 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 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE G 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 196 time to evaluate : 0.521 Fit side-chains REVERT: A 94 THR cc_start: 0.8908 (t) cc_final: 0.8689 (m) REVERT: A 99 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8702 (p) REVERT: C 106 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8198 (p0) REVERT: E 106 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8427 (p0) REVERT: I 99 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8718 (p) REVERT: M 106 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8034 (p0) REVERT: N 89 ASN cc_start: 0.8677 (m-40) cc_final: 0.8409 (m110) REVERT: N 106 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8014 (m110) REVERT: O 107 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8384 (p0) REVERT: P 91 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7939 (tt) REVERT: P 105 GLN cc_start: 0.8885 (tt0) cc_final: 0.8504 (tt0) REVERT: R 91 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7804 (tt) REVERT: S 105 GLN cc_start: 0.8825 (tm130) cc_final: 0.8616 (tm-30) REVERT: S 107 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.7980 (p0) outliers start: 69 outliers final: 42 residues processed: 223 average time/residue: 0.3485 time to fit residues: 87.3515 Evaluate side-chains 228 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 107 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN J 105 GLN J 107 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 107 ASN O 119 ASN P 89 ASN R 89 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.081 4884 Z= 0.911 Angle : 0.929 11.696 6611 Z= 0.444 Chirality : 0.060 0.341 770 Planarity : 0.004 0.022 880 Dihedral : 5.862 23.841 670 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 17.39 % Allowed : 23.91 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.003 PHE U 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 157 time to evaluate : 0.535 Fit side-chains REVERT: C 106 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7939 (p0) REVERT: D 106 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: I 99 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8828 (p) REVERT: J 103 SER cc_start: 0.8670 (t) cc_final: 0.8462 (t) REVERT: M 105 GLN cc_start: 0.8817 (tm130) cc_final: 0.8590 (tm-30) REVERT: M 106 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8223 (p0) REVERT: N 106 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7994 (m110) REVERT: O 107 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8363 (p0) REVERT: R 106 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7862 (m110) REVERT: S 107 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8444 (p0) REVERT: T 87 THR cc_start: 0.9090 (t) cc_final: 0.8782 (m) outliers start: 88 outliers final: 63 residues processed: 208 average time/residue: 0.3371 time to fit residues: 78.9001 Evaluate side-chains 218 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 147 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4884 Z= 0.237 Angle : 0.667 9.285 6611 Z= 0.302 Chirality : 0.043 0.205 770 Planarity : 0.002 0.024 880 Dihedral : 5.409 25.755 670 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 13.83 % Allowed : 25.49 % Favored : 60.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE C 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 182 time to evaluate : 0.526 Fit side-chains REVERT: C 106 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8438 (p0) REVERT: E 106 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8402 (p0) REVERT: K 99 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8980 (p) REVERT: M 106 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8237 (p0) REVERT: N 91 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7929 (tt) REVERT: N 106 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7917 (m110) REVERT: O 107 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8264 (p0) REVERT: P 91 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7843 (tt) REVERT: P 105 GLN cc_start: 0.8954 (tt0) cc_final: 0.8653 (tt0) REVERT: R 91 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7818 (tt) REVERT: R 106 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7832 (m110) REVERT: S 99 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9015 (p) REVERT: S 107 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8177 (p0) REVERT: T 87 THR cc_start: 0.9103 (t) cc_final: 0.8844 (m) outliers start: 70 outliers final: 41 residues processed: 218 average time/residue: 0.3356 time to fit residues: 82.2094 Evaluate side-chains 218 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 107 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN J 105 GLN J 107 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 112 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 105 GLN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 4884 Z= 0.431 Angle : 0.742 9.935 6611 Z= 0.338 Chirality : 0.047 0.271 770 Planarity : 0.003 0.025 880 Dihedral : 5.432 25.110 670 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 14.43 % Allowed : 24.11 % Favored : 61.46 % 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: -4.12 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE E 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 161 time to evaluate : 0.518 Fit side-chains REVERT: C 106 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8188 (p0) REVERT: D 91 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8189 (tt) REVERT: E 107 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8602 (p0) REVERT: I 94 THR cc_start: 0.8779 (t) cc_final: 0.8538 (m) REVERT: K 99 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8952 (p) REVERT: M 99 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.9200 (p) REVERT: M 106 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8445 (p0) REVERT: M 107 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8423 (p0) REVERT: N 106 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7942 (m110) REVERT: P 91 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7945 (mm) REVERT: R 91 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7890 (tt) REVERT: R 106 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7829 (m110) REVERT: S 99 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9033 (p) REVERT: T 87 THR cc_start: 0.9075 (t) cc_final: 0.8815 (m) REVERT: T 91 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8145 (tt) outliers start: 73 outliers final: 49 residues processed: 199 average time/residue: 0.3164 time to fit residues: 71.3171 Evaluate side-chains 220 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 158 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 106 ASN S 112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4884 Z= 0.190 Angle : 0.660 9.321 6611 Z= 0.293 Chirality : 0.041 0.197 770 Planarity : 0.002 0.020 880 Dihedral : 5.236 28.929 670 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 13.24 % Allowed : 25.30 % Favored : 61.46 % 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: -4.20 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 171 time to evaluate : 0.618 Fit side-chains REVERT: A 99 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8691 (p) REVERT: A 106 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7433 (p0) REVERT: C 106 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8295 (p0) REVERT: E 107 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8337 (p0) REVERT: K 99 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8991 (p) REVERT: N 91 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7941 (tt) REVERT: N 106 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7778 (m110) REVERT: R 91 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7931 (tt) REVERT: R 106 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7793 (m110) REVERT: S 99 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8727 (p) REVERT: T 91 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8085 (tt) REVERT: U 99 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8751 (m) outliers start: 67 outliers final: 42 residues processed: 206 average time/residue: 0.3238 time to fit residues: 75.4511 Evaluate side-chains 211 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 157 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 107 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 107 ASN C 111 GLN E 105 GLN E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN J 89 ASN J 105 GLN J 107 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 89 ASN L 107 ASN M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 4884 Z= 0.585 Angle : 0.799 10.406 6611 Z= 0.370 Chirality : 0.051 0.325 770 Planarity : 0.003 0.025 880 Dihedral : 5.359 24.624 668 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 14.43 % Allowed : 25.49 % Favored : 60.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE U 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 162 time to evaluate : 0.539 Fit side-chains REVERT: C 106 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8186 (p0) REVERT: K 99 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8983 (p) REVERT: M 106 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8511 (p0) REVERT: N 106 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7934 (m110) REVERT: P 91 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7922 (mm) REVERT: P 105 GLN cc_start: 0.9011 (tt0) cc_final: 0.8690 (tt0) REVERT: Q 94 THR cc_start: 0.8911 (t) cc_final: 0.8681 (t) REVERT: R 106 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7815 (m110) REVERT: S 99 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9030 (p) REVERT: T 87 THR cc_start: 0.9098 (t) cc_final: 0.8812 (m) outliers start: 73 outliers final: 49 residues processed: 199 average time/residue: 0.3822 time to fit residues: 85.8893 Evaluate side-chains 216 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 160 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN J 89 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4884 Z= 0.242 Angle : 0.698 9.774 6611 Z= 0.312 Chirality : 0.043 0.222 770 Planarity : 0.003 0.022 880 Dihedral : 5.198 27.593 668 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 11.26 % Allowed : 28.46 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE C 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 161 time to evaluate : 0.552 Fit side-chains REVERT: A 99 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8704 (p) REVERT: C 106 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8325 (p0) REVERT: N 106 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7904 (m110) REVERT: P 105 GLN cc_start: 0.8988 (tt0) cc_final: 0.8667 (tt0) REVERT: R 91 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7921 (tt) REVERT: R 106 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7786 (m110) REVERT: S 99 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.9049 (p) REVERT: S 107 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8216 (p0) REVERT: T 87 THR cc_start: 0.9063 (t) cc_final: 0.8863 (m) outliers start: 57 outliers final: 44 residues processed: 195 average time/residue: 0.3819 time to fit residues: 83.1813 Evaluate side-chains 211 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 160 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN C 111 GLN E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN J 105 GLN J 107 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 4884 Z= 0.572 Angle : 0.811 10.633 6611 Z= 0.374 Chirality : 0.052 0.340 770 Planarity : 0.003 0.024 880 Dihedral : 5.339 29.788 666 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 12.06 % Allowed : 29.25 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE U 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 157 time to evaluate : 0.602 Fit side-chains REVERT: M 106 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8464 (p0) REVERT: N 106 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7938 (m110) REVERT: Q 94 THR cc_start: 0.8963 (t) cc_final: 0.8639 (t) REVERT: R 106 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7811 (m110) REVERT: S 99 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9055 (p) REVERT: S 107 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8518 (p0) REVERT: T 87 THR cc_start: 0.9097 (t) cc_final: 0.8809 (m) outliers start: 61 outliers final: 45 residues processed: 190 average time/residue: 0.3667 time to fit residues: 77.9988 Evaluate side-chains 205 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 103 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN J 105 GLN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 GLN R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.075904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.067791 restraints weight = 7698.292| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.65 r_work: 0.2982 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4884 Z= 0.233 Angle : 0.705 9.616 6611 Z= 0.313 Chirality : 0.045 0.299 770 Planarity : 0.003 0.020 880 Dihedral : 4.963 35.137 664 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 10.87 % Allowed : 29.45 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.12), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE O 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.24 seconds wall clock time: 38 minutes 33.10 seconds (2313.10 seconds total)