Starting phenix.real_space_refine on Sat Aug 23 02:26:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4a_18883/08_2025/8r4a_18883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4a_18883/08_2025/8r4a_18883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r4a_18883/08_2025/8r4a_18883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4a_18883/08_2025/8r4a_18883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r4a_18883/08_2025/8r4a_18883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4a_18883/08_2025/8r4a_18883.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 5679 2.51 5 N 1800 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9225 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "C" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "D" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "E" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "G" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "H" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "I" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1025 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Time building chain proxies: 1.77, per 1000 atoms: 0.19 Number of scatterers: 9225 At special positions: 0 Unit cell: (100.88, 96.72, 71.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 1656 8.00 N 1800 7.00 C 5679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 116 " distance=2.01 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 128 " distance=2.04 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 116 " distance=2.01 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 128 " distance=2.04 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 116 " distance=2.01 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 81 " distance=2.03 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 128 " distance=2.04 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 116 " distance=2.01 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 81 " distance=2.03 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 128 " distance=2.04 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 116 " distance=2.01 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 77 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 128 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 116 " distance=2.01 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 81 " distance=2.03 Simple disulfide: pdb=" SG CYS F 77 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 128 " distance=2.04 Simple disulfide: pdb=" SG CYS G 30 " - pdb=" SG CYS G 116 " distance=2.01 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 81 " distance=2.03 Simple disulfide: pdb=" SG CYS G 77 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 128 " distance=2.04 Simple disulfide: pdb=" SG CYS H 30 " - pdb=" SG CYS H 116 " distance=2.01 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 81 " distance=2.03 Simple disulfide: pdb=" SG CYS H 77 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 128 " distance=2.04 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 116 " distance=2.01 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 81 " distance=2.03 Simple disulfide: pdb=" SG CYS I 77 " - pdb=" SG CYS I 95 " distance=2.03 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: 0.75 Conformation dependent library (CDL) restraints added in 287.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.725A pdb=" N ILE B 56 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 56 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 56 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 56 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE F 56 " --> pdb=" O GLY E 55 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE G 56 " --> pdb=" O GLY F 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE H 56 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE I 56 " --> pdb=" O GLY H 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.534A pdb=" N ILE A 59 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG B 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER A 61 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP B 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 63 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN B 66 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS A 65 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 59 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG C 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER B 61 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP C 64 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR B 63 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN C 66 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS B 65 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 59 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG D 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER C 61 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N TRP D 64 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR C 63 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN D 66 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS C 65 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE D 59 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG E 62 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER D 61 " --> pdb=" O ARG E 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP E 64 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 63 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN E 66 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS D 65 " --> pdb=" O ASN E 66 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE E 59 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG F 62 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER E 61 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP F 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR E 63 " --> pdb=" O TRP F 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN F 66 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS E 65 " --> pdb=" O ASN F 66 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE F 59 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG G 62 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER F 61 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP G 64 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR F 63 " --> pdb=" O TRP G 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN G 66 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS F 65 " --> pdb=" O ASN G 66 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE G 59 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG H 62 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER G 61 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP H 64 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR G 63 " --> pdb=" O TRP H 64 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASN H 66 " --> pdb=" O TYR G 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS G 65 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE H 59 " --> pdb=" O ASN I 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG I 62 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER H 61 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N TRP I 64 " --> pdb=" O SER H 61 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 63 " --> pdb=" O TRP I 64 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASN I 66 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS H 65 " --> pdb=" O ASN I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 74 through 79 removed outlier: 6.716A pdb=" N HIS B 78 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 79 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS C 78 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 79 " --> pdb=" O HIS C 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS D 78 " --> pdb=" O CYS C 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C 79 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS E 78 " --> pdb=" O CYS D 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU D 79 " --> pdb=" O HIS E 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS F 78 " --> pdb=" O CYS E 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 79 " --> pdb=" O HIS F 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS G 78 " --> pdb=" O CYS F 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU F 79 " --> pdb=" O HIS G 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS H 78 " --> pdb=" O CYS G 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU G 79 " --> pdb=" O HIS H 78 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS I 78 " --> pdb=" O CYS H 77 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU H 79 " --> pdb=" O HIS I 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AB1, first strand: chain 'A' and resid 124 through 126 96 hydrogen bonds defined for protein. 288 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: 1.02 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1503 1.30 - 1.43: 2718 1.43 - 1.56: 5076 1.56 - 1.69: 0 1.69 - 1.82: 108 Bond restraints: 9405 Sorted by residual: bond pdb=" C CYS D 6 " pdb=" O CYS D 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.69e+01 bond pdb=" C CYS I 6 " pdb=" O CYS I 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.69e+01 bond pdb=" C CYS F 6 " pdb=" O CYS F 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.69e+01 bond pdb=" C CYS G 6 " pdb=" O CYS G 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.68e+01 bond pdb=" C CYS E 6 " pdb=" O CYS E 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.68e+01 ... (remaining 9400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8771 1.87 - 3.75: 2561 3.75 - 5.62: 1160 5.62 - 7.50: 180 7.50 - 9.37: 36 Bond angle restraints: 12708 Sorted by residual: angle pdb=" CA ASP H 102 " pdb=" C ASP H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 118.16 122.86 -4.70 7.00e-01 2.04e+00 4.50e+01 angle pdb=" CA ASP F 102 " pdb=" C ASP F 102 " pdb=" N PRO F 103 " ideal model delta sigma weight residual 118.16 122.84 -4.68 7.00e-01 2.04e+00 4.47e+01 angle pdb=" CA ASP A 102 " pdb=" C ASP A 102 " pdb=" N PRO A 103 " ideal model delta sigma weight residual 118.16 122.82 -4.66 7.00e-01 2.04e+00 4.43e+01 angle pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 118.16 122.82 -4.66 7.00e-01 2.04e+00 4.43e+01 angle pdb=" CA ASP C 102 " pdb=" C ASP C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 118.16 122.81 -4.65 7.00e-01 2.04e+00 4.42e+01 ... (remaining 12703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 5067 15.61 - 31.22: 396 31.22 - 46.83: 117 46.83 - 62.43: 45 62.43 - 78.04: 36 Dihedral angle restraints: 5661 sinusoidal: 2322 harmonic: 3339 Sorted by residual: dihedral pdb=" CA ASN F 60 " pdb=" CB ASN F 60 " pdb=" CG ASN F 60 " pdb=" OD1 ASN F 60 " ideal model delta sinusoidal sigma weight residual -90.00 -159.22 69.22 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASN G 60 " pdb=" CB ASN G 60 " pdb=" CG ASN G 60 " pdb=" OD1 ASN G 60 " ideal model delta sinusoidal sigma weight residual -90.00 -159.22 69.22 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASN C 60 " pdb=" CB ASN C 60 " pdb=" CG ASN C 60 " pdb=" OD1 ASN C 60 " ideal model delta sinusoidal sigma weight residual -90.00 -159.21 69.21 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 561 0.064 - 0.128: 440 0.128 - 0.192: 205 0.192 - 0.256: 90 0.256 - 0.320: 9 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CA VAL C 121 " pdb=" N VAL C 121 " pdb=" C VAL C 121 " pdb=" CB VAL C 121 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL F 121 " pdb=" N VAL F 121 " pdb=" C VAL F 121 " pdb=" CB VAL F 121 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL B 121 " pdb=" N VAL B 121 " pdb=" C VAL B 121 " pdb=" CB VAL B 121 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1302 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 31 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU C 31 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 31 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA C 32 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 31 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU I 31 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU I 31 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA I 32 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 31 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU B 31 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU B 31 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 32 " 0.022 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3880 2.94 - 3.43: 9783 3.43 - 3.92: 16519 3.92 - 4.41: 20132 4.41 - 4.90: 35789 Nonbonded interactions: 86103 Sorted by model distance: nonbonded pdb=" N ASN G 118 " pdb=" O ASN G 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN E 118 " pdb=" O ASN E 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN H 118 " pdb=" O ASN H 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN A 118 " pdb=" O ASN A 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN B 118 " pdb=" O ASN B 118 " model vdw 2.451 2.496 ... (remaining 86098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.360 Find NCS groups from input model: 0.040 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.013 0.064 9441 Z= 0.988 Angle : 2.161 9.371 12780 Z= 1.562 Chirality : 0.105 0.320 1305 Planarity : 0.011 0.037 1674 Dihedral : 15.072 78.043 3429 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.27 (0.13), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.10), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 14 TYR 0.018 0.003 TYR G 63 PHE 0.016 0.003 PHE H 3 TRP 0.024 0.004 TRP G 112 HIS 0.007 0.005 HIS H 78 Details of bonding type rmsd covalent geometry : bond 0.01314 ( 9405) covalent geometry : angle 2.16272 (12708) SS BOND : bond 0.01280 ( 36) SS BOND : angle 1.87167 ( 72) hydrogen bonds : bond 0.27857 ( 96) hydrogen bonds : angle 9.95736 ( 288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.390 Fit side-chains REVERT: B 67 ASP cc_start: 0.7893 (t0) cc_final: 0.7486 (t0) REVERT: B 98 ARG cc_start: 0.7405 (ttm110) cc_final: 0.7056 (ttm170) REVERT: C 98 ARG cc_start: 0.7339 (ttm110) cc_final: 0.6969 (ttm170) REVERT: D 29 MET cc_start: 0.7516 (mtt) cc_final: 0.7244 (mtt) REVERT: D 43 THR cc_start: 0.8798 (p) cc_final: 0.8502 (m) REVERT: E 74 VAL cc_start: 0.8842 (p) cc_final: 0.8620 (t) REVERT: F 29 MET cc_start: 0.7546 (mtt) cc_final: 0.7334 (mtt) REVERT: G 74 VAL cc_start: 0.8791 (p) cc_final: 0.8554 (t) REVERT: I 45 TYR cc_start: 0.9011 (m-80) cc_final: 0.8705 (m-80) REVERT: I 97 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7743 (tmmt) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.4956 time to fit residues: 158.2204 Evaluate side-chains 193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 58 GLN B 44 ASN B 58 GLN B 104 GLN C 44 ASN C 58 GLN C 88 ASN D 27 ASN D 44 ASN D 58 GLN D 75 ASN E 44 ASN E 58 GLN ** E 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN F 44 ASN ** F 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN H 44 ASN H 58 GLN H 104 GLN H 126 GLN I 44 ASN I 104 GLN I 114 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.094954 restraints weight = 10878.599| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.32 r_work: 0.3229 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9441 Z= 0.181 Angle : 0.834 10.154 12780 Z= 0.452 Chirality : 0.052 0.168 1305 Planarity : 0.004 0.029 1674 Dihedral : 7.784 50.585 1350 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.88 % Allowed : 19.34 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.21 (0.15), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 10 TYR 0.015 0.002 TYR F 54 PHE 0.024 0.005 PHE D 3 TRP 0.016 0.002 TRP B 112 HIS 0.003 0.002 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9405) covalent geometry : angle 0.83447 (12708) SS BOND : bond 0.00327 ( 36) SS BOND : angle 0.78299 ( 72) hydrogen bonds : bond 0.07883 ( 96) hydrogen bonds : angle 5.64842 ( 288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 0.228 Fit side-chains REVERT: B 12 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7458 (tt) REVERT: B 67 ASP cc_start: 0.8233 (t0) cc_final: 0.8013 (t0) REVERT: C 12 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7599 (tt) REVERT: C 62 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: C 98 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7692 (ttm170) REVERT: C 106 ILE cc_start: 0.8662 (mp) cc_final: 0.8432 (mt) REVERT: C 113 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8107 (mtm-85) REVERT: D 29 MET cc_start: 0.8050 (mtt) cc_final: 0.7827 (mtt) REVERT: D 113 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8234 (mtm-85) REVERT: E 12 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7706 (tt) REVERT: E 98 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7887 (ttm170) REVERT: F 117 GLN cc_start: 0.8550 (pt0) cc_final: 0.8241 (pt0) REVERT: G 12 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7795 (tt) REVERT: I 115 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8073 (ttt90) REVERT: I 118 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7723 (t0) outliers start: 55 outliers final: 20 residues processed: 209 average time/residue: 0.3766 time to fit residues: 85.2134 Evaluate side-chains 179 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 115 ARG Chi-restraints excluded: chain I residue 118 ASN Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 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 78 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN E 88 ASN F 88 ASN F 104 GLN H 88 ASN H 104 GLN H 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.109591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091640 restraints weight = 10853.909| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.36 r_work: 0.3166 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9441 Z= 0.150 Angle : 0.747 8.915 12780 Z= 0.399 Chirality : 0.049 0.169 1305 Planarity : 0.003 0.028 1674 Dihedral : 7.115 38.458 1350 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.56 % Allowed : 22.33 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.23 (0.15), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 10 TYR 0.011 0.002 TYR F 54 PHE 0.018 0.003 PHE F 3 TRP 0.014 0.002 TRP B 112 HIS 0.004 0.002 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9405) covalent geometry : angle 0.74802 (12708) SS BOND : bond 0.00383 ( 36) SS BOND : angle 0.63783 ( 72) hydrogen bonds : bond 0.06910 ( 96) hydrogen bonds : angle 5.66651 ( 288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 0.326 Fit side-chains REVERT: B 12 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7540 (tt) REVERT: B 67 ASP cc_start: 0.8218 (t0) cc_final: 0.8008 (t0) REVERT: C 12 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7703 (tt) REVERT: C 62 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7934 (ttp80) REVERT: C 98 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7860 (ttm170) REVERT: C 113 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: D 29 MET cc_start: 0.8124 (mtt) cc_final: 0.7904 (mtt) REVERT: D 62 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8123 (ttp-170) REVERT: E 12 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7752 (tt) REVERT: F 117 GLN cc_start: 0.8589 (pt0) cc_final: 0.8211 (pt0) outliers start: 52 outliers final: 27 residues processed: 188 average time/residue: 0.4473 time to fit residues: 90.3640 Evaluate side-chains 181 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN D 78 HIS E 78 HIS E 88 ASN F 78 HIS ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS G 88 ASN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN H 104 GLN I 78 HIS ** I 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084835 restraints weight = 10699.582| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.38 r_work: 0.3051 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 9441 Z= 0.330 Angle : 0.878 10.853 12780 Z= 0.465 Chirality : 0.054 0.180 1305 Planarity : 0.005 0.039 1674 Dihedral : 7.633 46.802 1350 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 6.62 % Allowed : 22.76 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 10 TYR 0.015 0.002 TYR F 54 PHE 0.017 0.003 PHE F 3 TRP 0.017 0.002 TRP B 112 HIS 0.007 0.002 HIS E 78 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 9405) covalent geometry : angle 0.87707 (12708) SS BOND : bond 0.00680 ( 36) SS BOND : angle 1.09068 ( 72) hydrogen bonds : bond 0.08238 ( 96) hydrogen bonds : angle 6.26747 ( 288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 148 time to evaluate : 0.238 Fit side-chains REVERT: A 29 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8261 (mmt) REVERT: A 35 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: A 91 ASP cc_start: 0.8492 (m-30) cc_final: 0.8285 (m-30) REVERT: B 12 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 67 ASP cc_start: 0.8329 (t0) cc_final: 0.8093 (t0) REVERT: C 12 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7930 (tt) REVERT: C 62 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7481 (ttm170) REVERT: C 98 ARG cc_start: 0.8283 (ttm110) cc_final: 0.8000 (ttm170) REVERT: C 113 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8278 (mtm-85) REVERT: D 62 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8088 (ttp-170) REVERT: E 12 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7860 (tt) REVERT: F 12 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7937 (tt) REVERT: H 12 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7971 (tt) REVERT: I 62 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7850 (ttt90) REVERT: I 115 ARG cc_start: 0.8401 (ttt90) cc_final: 0.8141 (ttt90) outliers start: 62 outliers final: 36 residues processed: 184 average time/residue: 0.4566 time to fit residues: 89.9956 Evaluate side-chains 190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 91 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086559 restraints weight = 10510.179| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.36 r_work: 0.3087 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9441 Z= 0.202 Angle : 0.763 8.483 12780 Z= 0.409 Chirality : 0.050 0.177 1305 Planarity : 0.004 0.034 1674 Dihedral : 7.312 41.538 1350 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.88 % Allowed : 24.15 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.27 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 10 TYR 0.011 0.002 TYR A 54 PHE 0.017 0.003 PHE G 3 TRP 0.014 0.002 TRP B 112 HIS 0.003 0.001 HIS H 78 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9405) covalent geometry : angle 0.76315 (12708) SS BOND : bond 0.00516 ( 36) SS BOND : angle 0.79572 ( 72) hydrogen bonds : bond 0.07277 ( 96) hydrogen bonds : angle 6.10067 ( 288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.312 Fit side-chains REVERT: A 35 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: A 91 ASP cc_start: 0.8526 (m-30) cc_final: 0.8316 (m-30) REVERT: B 12 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7673 (tt) REVERT: B 67 ASP cc_start: 0.8320 (t0) cc_final: 0.8017 (t0) REVERT: C 12 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7873 (tt) REVERT: C 62 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7820 (ttp80) REVERT: C 98 ARG cc_start: 0.8283 (ttm110) cc_final: 0.8003 (ttm170) REVERT: C 113 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8274 (mtm-85) REVERT: D 62 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8090 (ttp-170) REVERT: E 12 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7767 (tt) REVERT: E 53 ASP cc_start: 0.8399 (p0) cc_final: 0.8181 (p0) REVERT: F 12 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7885 (tt) REVERT: F 29 MET cc_start: 0.8561 (mtt) cc_final: 0.8350 (mmt) REVERT: F 117 GLN cc_start: 0.8777 (pt0) cc_final: 0.8389 (pt0) outliers start: 55 outliers final: 33 residues processed: 175 average time/residue: 0.4526 time to fit residues: 85.3509 Evaluate side-chains 186 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.087568 restraints weight = 10513.958| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.41 r_work: 0.3101 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9441 Z= 0.161 Angle : 0.717 8.186 12780 Z= 0.384 Chirality : 0.049 0.174 1305 Planarity : 0.003 0.039 1674 Dihedral : 7.079 35.560 1350 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.30 % Allowed : 22.97 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.23 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 10 TYR 0.011 0.002 TYR A 54 PHE 0.015 0.002 PHE G 3 TRP 0.013 0.002 TRP B 112 HIS 0.002 0.001 HIS H 78 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9405) covalent geometry : angle 0.71696 (12708) SS BOND : bond 0.00411 ( 36) SS BOND : angle 0.64668 ( 72) hydrogen bonds : bond 0.06747 ( 96) hydrogen bonds : angle 5.92243 ( 288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 154 time to evaluate : 0.340 Fit side-chains REVERT: A 35 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: B 12 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7699 (tt) REVERT: B 17 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8593 (mtm) REVERT: B 67 ASP cc_start: 0.8297 (t0) cc_final: 0.7984 (t0) REVERT: C 12 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7836 (tt) REVERT: C 62 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7842 (ttp80) REVERT: C 98 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7943 (ttm170) REVERT: C 113 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8263 (mtm-85) REVERT: D 62 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8108 (ttp-170) REVERT: E 12 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7743 (tt) REVERT: F 12 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7859 (tt) REVERT: F 117 GLN cc_start: 0.8765 (pt0) cc_final: 0.8449 (pt0) REVERT: H 17 MET cc_start: 0.8807 (mtm) cc_final: 0.8593 (mtm) outliers start: 59 outliers final: 35 residues processed: 190 average time/residue: 0.4477 time to fit residues: 91.5410 Evaluate side-chains 192 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 0.0370 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 HIS H 104 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087576 restraints weight = 10777.274| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.38 r_work: 0.3112 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9441 Z= 0.166 Angle : 0.717 8.581 12780 Z= 0.383 Chirality : 0.049 0.172 1305 Planarity : 0.003 0.043 1674 Dihedral : 7.000 34.029 1350 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.88 % Allowed : 23.08 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.23 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 10 TYR 0.011 0.002 TYR B 124 PHE 0.014 0.002 PHE G 3 TRP 0.013 0.002 TRP B 112 HIS 0.002 0.001 HIS H 78 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9405) covalent geometry : angle 0.71749 (12708) SS BOND : bond 0.00407 ( 36) SS BOND : angle 0.66283 ( 72) hydrogen bonds : bond 0.06696 ( 96) hydrogen bonds : angle 5.79799 ( 288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 151 time to evaluate : 0.249 Fit side-chains REVERT: A 29 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8181 (mmt) REVERT: A 35 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: B 12 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7716 (tt) REVERT: B 17 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: B 67 ASP cc_start: 0.8265 (t0) cc_final: 0.7961 (t0) REVERT: C 12 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7845 (tt) REVERT: C 62 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7695 (ttp80) REVERT: C 98 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7944 (ttm170) REVERT: C 113 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8277 (mtm-85) REVERT: D 62 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8122 (ttp-170) REVERT: E 12 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7774 (tt) REVERT: F 12 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7896 (tt) REVERT: F 117 GLN cc_start: 0.8732 (pt0) cc_final: 0.8428 (pt0) REVERT: I 35 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8150 (mp0) outliers start: 55 outliers final: 38 residues processed: 179 average time/residue: 0.4051 time to fit residues: 78.2143 Evaluate side-chains 197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 148 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN H 104 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085551 restraints weight = 10459.933| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.39 r_work: 0.3073 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9441 Z= 0.241 Angle : 0.777 9.244 12780 Z= 0.413 Chirality : 0.051 0.182 1305 Planarity : 0.004 0.047 1674 Dihedral : 7.209 38.081 1350 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.56 % Allowed : 23.50 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 10 TYR 0.014 0.002 TYR B 124 PHE 0.015 0.002 PHE G 3 TRP 0.013 0.002 TRP B 112 HIS 0.002 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 9405) covalent geometry : angle 0.77636 (12708) SS BOND : bond 0.00542 ( 36) SS BOND : angle 0.84259 ( 72) hydrogen bonds : bond 0.07290 ( 96) hydrogen bonds : angle 5.89188 ( 288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.303 Fit side-chains REVERT: A 29 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8236 (mmt) REVERT: A 35 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: B 12 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 67 ASP cc_start: 0.8296 (t0) cc_final: 0.7991 (t0) REVERT: C 12 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7923 (tt) REVERT: C 62 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7863 (ttp80) REVERT: C 98 ARG cc_start: 0.8217 (ttm110) cc_final: 0.7928 (ttm170) REVERT: C 113 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8255 (mtm-85) REVERT: D 62 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8128 (ttp-170) REVERT: E 12 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7839 (tt) REVERT: F 12 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7944 (tt) REVERT: I 35 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8114 (mp0) outliers start: 52 outliers final: 40 residues processed: 178 average time/residue: 0.4118 time to fit residues: 79.2144 Evaluate side-chains 196 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 104 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087678 restraints weight = 10733.835| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.38 r_work: 0.3116 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9441 Z= 0.147 Angle : 0.702 9.112 12780 Z= 0.376 Chirality : 0.049 0.173 1305 Planarity : 0.003 0.054 1674 Dihedral : 6.957 33.372 1350 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.45 % Allowed : 24.04 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.29 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 10 TYR 0.014 0.001 TYR B 124 PHE 0.012 0.002 PHE D 3 TRP 0.013 0.002 TRP D 28 HIS 0.001 0.000 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9405) covalent geometry : angle 0.70235 (12708) SS BOND : bond 0.00374 ( 36) SS BOND : angle 0.56997 ( 72) hydrogen bonds : bond 0.06383 ( 96) hydrogen bonds : angle 5.70640 ( 288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.304 Fit side-chains REVERT: A 29 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8179 (mmt) REVERT: A 35 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: B 12 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7682 (tt) REVERT: B 17 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8608 (mtm) REVERT: C 12 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7817 (tt) REVERT: C 62 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7677 (ttp80) REVERT: C 98 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7898 (ttm170) REVERT: C 113 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8264 (mtm-85) REVERT: D 62 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8116 (ttp-170) REVERT: E 12 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7795 (tt) REVERT: F 12 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7903 (tt) REVERT: F 117 GLN cc_start: 0.8742 (pt0) cc_final: 0.8376 (pt0) outliers start: 51 outliers final: 39 residues processed: 176 average time/residue: 0.4198 time to fit residues: 79.7517 Evaluate side-chains 193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 62 optimal weight: 0.4980 chunk 81 optimal weight: 0.0770 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 104 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.090243 restraints weight = 10656.618| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.39 r_work: 0.3164 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9441 Z= 0.101 Angle : 0.658 9.469 12780 Z= 0.352 Chirality : 0.048 0.164 1305 Planarity : 0.003 0.059 1674 Dihedral : 6.677 27.538 1350 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.27 % Allowed : 25.00 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.27 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 10 TYR 0.012 0.001 TYR B 124 PHE 0.012 0.002 PHE D 3 TRP 0.014 0.002 TRP D 28 HIS 0.001 0.000 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9405) covalent geometry : angle 0.65882 (12708) SS BOND : bond 0.00262 ( 36) SS BOND : angle 0.42155 ( 72) hydrogen bonds : bond 0.05603 ( 96) hydrogen bonds : angle 5.53750 ( 288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.255 Fit side-chains REVERT: A 35 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: B 12 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7648 (tt) REVERT: B 17 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: C 12 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7695 (tt) REVERT: C 98 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7858 (ttm170) REVERT: C 113 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8232 (mtm-85) REVERT: D 29 MET cc_start: 0.8169 (mtp) cc_final: 0.7933 (mmt) REVERT: E 12 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7715 (tt) REVERT: F 12 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7788 (tt) REVERT: F 117 GLN cc_start: 0.8640 (pt0) cc_final: 0.8204 (pt0) REVERT: H 17 MET cc_start: 0.8731 (mtm) cc_final: 0.8486 (mtm) outliers start: 40 outliers final: 27 residues processed: 175 average time/residue: 0.4152 time to fit residues: 78.8553 Evaluate side-chains 182 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 114 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 86 GLN H 104 GLN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089110 restraints weight = 10559.465| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.38 r_work: 0.3148 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9441 Z= 0.132 Angle : 0.681 9.569 12780 Z= 0.362 Chirality : 0.048 0.169 1305 Planarity : 0.003 0.059 1674 Dihedral : 6.736 29.259 1350 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.74 % Allowed : 25.85 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 10 TYR 0.013 0.001 TYR H 124 PHE 0.011 0.002 PHE D 3 TRP 0.011 0.001 TRP H 112 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9405) covalent geometry : angle 0.68163 (12708) SS BOND : bond 0.00322 ( 36) SS BOND : angle 0.54933 ( 72) hydrogen bonds : bond 0.05989 ( 96) hydrogen bonds : angle 5.54185 ( 288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2754.74 seconds wall clock time: 47 minutes 49.29 seconds (2869.29 seconds total)