Starting phenix.real_space_refine on Mon May 12 16:35:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4a_18883/05_2025/8r4a_18883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4a_18883/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r4a_18883/05_2025/8r4a_18883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4a_18883/05_2025/8r4a_18883.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4a_18883/05_2025/8r4a_18883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4a_18883/05_2025/8r4a_18883.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.04, per 1000 atoms: 0.65 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 2.29 Time building geometry restraints manager: 2.77 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.570 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.13), 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 TRP 0.024 0.004 TRP G 112 HIS 0.007 0.005 HIS H 78 PHE 0.016 0.003 PHE H 3 TYR 0.018 0.003 TYR G 63 ARG 0.004 0.001 ARG I 14 Details of bonding type rmsd hydrogen bonds : bond 0.27857 ( 96) hydrogen bonds : angle 9.95736 ( 288) SS BOND : bond 0.01280 ( 36) SS BOND : angle 1.87167 ( 72) covalent geometry : bond 0.01314 ( 9405) covalent geometry : angle 2.16272 (12708) *********************** 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 : 0.959 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: 0.7214 (mtt) REVERT: D 43 THR cc_start: 0.8798 (p) cc_final: 0.8503 (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: 0.7336 (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: 0.8704 (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: 1.2108 time to fit residues: 386.6355 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 : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN I 44 ASN I 104 GLN I 114 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095056 restraints weight = 10774.801| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.31 r_work: 0.3230 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2364 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= 0.188 Angle : 0.834 9.993 12780 Z= 0.451 Chirality : 0.052 0.167 1305 Planarity : 0.004 0.029 1674 Dihedral : 7.774 51.157 1350 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.77 % Allowed : 19.66 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.15), residues: 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 TRP 0.016 0.002 TRP B 112 HIS 0.003 0.001 HIS B 78 PHE 0.024 0.005 PHE D 3 TYR 0.015 0.002 TYR F 54 ARG 0.005 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.08172 ( 96) hydrogen bonds : angle 5.67474 ( 288) SS BOND : bond 0.00340 ( 36) SS BOND : angle 0.66678 ( 72) covalent geometry : bond 0.00431 ( 9405) covalent geometry : angle 0.83488 (12708) *********************** 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 224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.985 Fit side-chains REVERT: B 12 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7440 (tt) REVERT: B 67 ASP cc_start: 0.8232 (t0) cc_final: 0.8008 (t0) REVERT: C 12 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7572 (tt) REVERT: C 62 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7806 (ttm170) REVERT: C 98 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7703 (ttm170) REVERT: C 106 ILE cc_start: 0.8658 (mp) cc_final: 0.8431 (mt) REVERT: C 113 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8067 (mtm-85) REVERT: D 29 MET cc_start: 0.8119 (mtt) cc_final: 0.7876 (mtt) REVERT: D 113 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: E 12 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7689 (tt) REVERT: E 98 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7890 (ttm170) REVERT: F 117 GLN cc_start: 0.8569 (pt0) cc_final: 0.8265 (pt0) REVERT: I 115 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (ttt90) outliers start: 54 outliers final: 19 residues processed: 206 average time/residue: 0.9866 time to fit residues: 220.5043 Evaluate side-chains 181 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 74 VAL 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 59 ILE Chi-restraints excluded: chain I residue 115 ARG 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 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 78 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN E 88 ASN F 88 ASN F 104 GLN ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 ASN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 ASN H 114 ASN I 78 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089514 restraints weight = 10937.458| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.35 r_work: 0.3134 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9441 Z= 0.203 Angle : 0.795 9.972 12780 Z= 0.426 Chirality : 0.051 0.176 1305 Planarity : 0.004 0.027 1674 Dihedral : 7.390 43.509 1350 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 6.09 % Allowed : 21.47 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.15), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 28 HIS 0.005 0.002 HIS B 78 PHE 0.019 0.003 PHE F 3 TYR 0.013 0.002 TYR F 54 ARG 0.007 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.07569 ( 96) hydrogen bonds : angle 5.82600 ( 288) SS BOND : bond 0.00496 ( 36) SS BOND : angle 0.76693 ( 72) covalent geometry : bond 0.00464 ( 9405) covalent geometry : angle 0.79549 (12708) *********************** 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 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 1.097 Fit side-chains REVERT: B 12 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7565 (tt) REVERT: C 12 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7744 (tt) REVERT: C 62 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7926 (ttp80) REVERT: C 98 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7880 (ttm170) REVERT: C 113 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8292 (mtm-85) REVERT: D 29 MET cc_start: 0.8215 (mtt) cc_final: 0.7991 (mtt) REVERT: D 62 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8104 (ttp-170) REVERT: E 12 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7825 (tt) REVERT: F 117 GLN cc_start: 0.8656 (pt0) cc_final: 0.8279 (pt0) REVERT: H 12 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7838 (tt) REVERT: I 10 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8271 (mtp-110) REVERT: I 118 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7746 (t0) outliers start: 57 outliers final: 27 residues processed: 194 average time/residue: 1.0929 time to fit residues: 227.7708 Evaluate side-chains 185 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 29 MET 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 70 THR Chi-restraints excluded: chain I residue 118 ASN 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 64 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 0.0020 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 88 ASN C 114 ASN E 88 ASN F 78 HIS G 78 HIS G 88 ASN H 88 ASN H 104 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.105349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.086557 restraints weight = 10515.328| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.39 r_work: 0.3081 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9441 Z= 0.245 Angle : 0.806 9.371 12780 Z= 0.429 Chirality : 0.051 0.179 1305 Planarity : 0.004 0.028 1674 Dihedral : 7.409 42.579 1350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.09 % Allowed : 23.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 112 HIS 0.005 0.002 HIS G 78 PHE 0.017 0.003 PHE F 3 TYR 0.013 0.002 TYR C 54 ARG 0.010 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.07634 ( 96) hydrogen bonds : angle 6.05798 ( 288) SS BOND : bond 0.00560 ( 36) SS BOND : angle 0.91723 ( 72) covalent geometry : bond 0.00557 ( 9405) covalent geometry : angle 0.80541 (12708) *********************** 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 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 1.079 Fit side-chains REVERT: A 29 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8245 (mmt) REVERT: A 35 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: A 91 ASP cc_start: 0.8472 (m-30) cc_final: 0.8258 (m-30) REVERT: B 12 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7630 (tt) REVERT: B 97 LYS cc_start: 0.8375 (ttpp) cc_final: 0.8171 (mtpm) REVERT: C 12 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7860 (tt) REVERT: C 62 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: C 98 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7937 (ttm170) REVERT: C 113 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8278 (mtm-85) REVERT: D 62 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8108 (ttp-170) REVERT: E 12 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7798 (tt) REVERT: F 12 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7912 (tt) REVERT: F 117 GLN cc_start: 0.8758 (pt0) cc_final: 0.8420 (pt0) REVERT: H 12 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7926 (tt) REVERT: I 10 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8261 (mtp-110) REVERT: I 53 ASP cc_start: 0.8744 (p0) cc_final: 0.8416 (p0) REVERT: I 62 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7898 (ttt90) REVERT: I 115 ARG cc_start: 0.8376 (ttt90) cc_final: 0.8091 (ttt90) outliers start: 57 outliers final: 33 residues processed: 179 average time/residue: 1.0939 time to fit residues: 210.4337 Evaluate side-chains 190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 11 THR 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 12 LEU Chi-restraints excluded: chain H residue 59 ILE 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 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 30 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 88 ASN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087229 restraints weight = 10450.584| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.39 r_work: 0.3095 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9441 Z= 0.192 Angle : 0.746 8.370 12780 Z= 0.400 Chirality : 0.050 0.172 1305 Planarity : 0.004 0.036 1674 Dihedral : 7.206 38.666 1350 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.98 % Allowed : 22.86 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (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 TRP 0.014 0.002 TRP B 112 HIS 0.004 0.001 HIS E 78 PHE 0.017 0.003 PHE G 3 TYR 0.011 0.002 TYR A 54 ARG 0.011 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.07098 ( 96) hydrogen bonds : angle 6.02022 ( 288) SS BOND : bond 0.00495 ( 36) SS BOND : angle 0.77071 ( 72) covalent geometry : bond 0.00429 ( 9405) covalent geometry : angle 0.74557 (12708) *********************** 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 209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 0.941 Fit side-chains REVERT: A 35 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: A 91 ASP cc_start: 0.8528 (m-30) cc_final: 0.8316 (m-30) REVERT: B 12 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7668 (tt) REVERT: C 12 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7837 (tt) REVERT: C 62 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7839 (ttp80) REVERT: C 98 ARG cc_start: 0.8309 (ttm110) cc_final: 0.8030 (ttm170) REVERT: C 113 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8279 (mtm-85) REVERT: D 62 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8112 (ttp-170) REVERT: E 12 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7792 (tt) REVERT: F 12 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7893 (tt) REVERT: F 117 GLN cc_start: 0.8753 (pt0) cc_final: 0.8447 (pt0) REVERT: H 17 MET cc_start: 0.8817 (mtm) cc_final: 0.8607 (mtm) REVERT: I 10 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8244 (mtp-110) REVERT: I 35 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: I 53 ASP cc_start: 0.8731 (p0) cc_final: 0.8422 (p0) outliers start: 56 outliers final: 33 residues processed: 184 average time/residue: 1.0675 time to fit residues: 211.5988 Evaluate side-chains 190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET 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 12 LEU 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 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 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 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 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 78 HIS C 104 GLN D 78 HIS D 123 GLN E 78 HIS E 86 GLN H 78 HIS ** H 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.102324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083562 restraints weight = 10595.101| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.38 r_work: 0.3037 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 9441 Z= 0.354 Angle : 0.870 10.017 12780 Z= 0.460 Chirality : 0.054 0.198 1305 Planarity : 0.005 0.043 1674 Dihedral : 7.644 46.460 1350 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 7.16 % Allowed : 22.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (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 TRP 0.017 0.002 TRP B 112 HIS 0.008 0.002 HIS E 78 PHE 0.018 0.003 PHE G 3 TYR 0.013 0.002 TYR F 54 ARG 0.014 0.001 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.08204 ( 96) hydrogen bonds : angle 6.23995 ( 288) SS BOND : bond 0.00738 ( 36) SS BOND : angle 1.08956 ( 72) covalent geometry : bond 0.00801 ( 9405) covalent geometry : angle 0.86848 (12708) *********************** 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 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 1.043 Fit side-chains REVERT: A 35 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: B 12 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7760 (tt) REVERT: C 12 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 62 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: C 106 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8662 (mp) REVERT: C 113 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8285 (mtm-85) REVERT: D 62 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8103 (ttp-170) REVERT: E 12 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7970 (tt) REVERT: F 12 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8019 (tt) REVERT: I 35 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: I 53 ASP cc_start: 0.8754 (p0) cc_final: 0.8474 (p0) REVERT: I 62 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7833 (ttt90) outliers start: 67 outliers final: 41 residues processed: 185 average time/residue: 1.0956 time to fit residues: 218.2291 Evaluate side-chains 197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 29 MET 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 70 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 11 THR 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 85 LEU Chi-restraints excluded: chain E residue 118 ASN 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 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 35 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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** D 123 GLN E 86 GLN H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.087772 restraints weight = 10760.915| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.37 r_work: 0.3112 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9441 Z= 0.145 Angle : 0.712 8.362 12780 Z= 0.383 Chirality : 0.049 0.177 1305 Planarity : 0.003 0.047 1674 Dihedral : 7.159 37.169 1350 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.34 % Allowed : 24.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 28 HIS 0.002 0.001 HIS E 78 PHE 0.014 0.002 PHE D 3 TYR 0.011 0.001 TYR B 124 ARG 0.013 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.06711 ( 96) hydrogen bonds : angle 5.89222 ( 288) SS BOND : bond 0.00391 ( 36) SS BOND : angle 0.63186 ( 72) covalent geometry : bond 0.00315 ( 9405) covalent geometry : angle 0.71289 (12708) *********************** 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: 50 poor density : 156 time to evaluate : 1.012 Fit side-chains REVERT: A 35 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: B 12 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7655 (tt) REVERT: B 17 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8593 (mtm) REVERT: C 12 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 62 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7803 (ttp80) REVERT: C 113 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8315 (mtm-85) REVERT: D 62 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8150 (ttp-170) REVERT: E 12 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7818 (tt) REVERT: F 12 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7878 (tt) REVERT: F 117 GLN cc_start: 0.8774 (pt0) cc_final: 0.8328 (pt0) REVERT: H 17 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8654 (mtm) REVERT: I 53 ASP cc_start: 0.8685 (p0) cc_final: 0.8408 (p0) outliers start: 50 outliers final: 30 residues processed: 182 average time/residue: 0.9629 time to fit residues: 190.0787 Evaluate side-chains 191 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET 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 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 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 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 17 MET 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 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** D 123 GLN E 86 GLN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.086773 restraints weight = 10915.259| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.39 r_work: 0.3097 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9441 Z= 0.182 Angle : 0.733 8.914 12780 Z= 0.391 Chirality : 0.049 0.175 1305 Planarity : 0.004 0.049 1674 Dihedral : 7.131 35.934 1350 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.24 % Allowed : 24.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 112 HIS 0.002 0.001 HIS B 78 PHE 0.013 0.002 PHE G 3 TYR 0.012 0.002 TYR B 124 ARG 0.013 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.06872 ( 96) hydrogen bonds : angle 5.77700 ( 288) SS BOND : bond 0.00444 ( 36) SS BOND : angle 0.72502 ( 72) covalent geometry : bond 0.00403 ( 9405) covalent geometry : angle 0.73343 (12708) *********************** 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 200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.959 Fit side-chains REVERT: A 35 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8263 (mt-10) REVERT: B 12 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7726 (tt) REVERT: C 12 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7885 (tt) REVERT: C 62 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7846 (ttp80) REVERT: C 113 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8314 (mtm-85) REVERT: D 62 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8129 (ttp-170) REVERT: E 12 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7834 (tt) REVERT: F 12 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7904 (tt) REVERT: F 117 GLN cc_start: 0.8796 (pt0) cc_final: 0.8448 (pt0) REVERT: H 17 MET cc_start: 0.8846 (mtm) cc_final: 0.8621 (mtm) REVERT: I 35 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: I 53 ASP cc_start: 0.8691 (p0) cc_final: 0.8436 (p0) outliers start: 49 outliers final: 36 residues processed: 177 average time/residue: 1.0097 time to fit residues: 193.5698 Evaluate side-chains 194 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 29 MET 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 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 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 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 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 130 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086291 restraints weight = 10719.226| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.40 r_work: 0.3090 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9441 Z= 0.203 Angle : 0.748 9.052 12780 Z= 0.399 Chirality : 0.050 0.186 1305 Planarity : 0.004 0.053 1674 Dihedral : 7.167 36.677 1350 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.34 % Allowed : 24.36 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 112 HIS 0.002 0.001 HIS B 78 PHE 0.014 0.002 PHE G 3 TYR 0.013 0.002 TYR B 124 ARG 0.015 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.07023 ( 96) hydrogen bonds : angle 5.74288 ( 288) SS BOND : bond 0.00481 ( 36) SS BOND : angle 0.76096 ( 72) covalent geometry : bond 0.00452 ( 9405) covalent geometry : angle 0.74752 (12708) *********************** 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 198 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.094 Fit side-chains REVERT: A 35 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: B 12 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7737 (tt) REVERT: C 12 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 62 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7853 (ttp80) REVERT: C 113 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8321 (mtm-85) REVERT: D 62 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8125 (ttp-170) REVERT: E 12 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7841 (tt) REVERT: F 12 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7915 (tt) REVERT: F 117 GLN cc_start: 0.8797 (pt0) cc_final: 0.8440 (pt0) REVERT: I 35 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: I 53 ASP cc_start: 0.8705 (p0) cc_final: 0.8458 (p0) outliers start: 50 outliers final: 39 residues processed: 172 average time/residue: 1.0121 time to fit residues: 188.3632 Evaluate side-chains 194 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 29 MET 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 2 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.086919 restraints weight = 10819.136| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.37 r_work: 0.3105 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9441 Z= 0.181 Angle : 0.735 9.260 12780 Z= 0.391 Chirality : 0.049 0.189 1305 Planarity : 0.004 0.053 1674 Dihedral : 7.110 35.382 1350 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.13 % Allowed : 24.68 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.17), 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 TRP 0.012 0.002 TRP B 112 HIS 0.002 0.001 HIS B 78 PHE 0.013 0.002 PHE G 3 TYR 0.014 0.002 TYR B 124 ARG 0.014 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.06809 ( 96) hydrogen bonds : angle 5.69790 ( 288) SS BOND : bond 0.00431 ( 36) SS BOND : angle 0.69573 ( 72) covalent geometry : bond 0.00400 ( 9405) covalent geometry : angle 0.73483 (12708) ********************** 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 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.956 Fit side-chains REVERT: A 35 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: B 12 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7720 (tt) REVERT: C 12 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7940 (tt) REVERT: C 62 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: C 113 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8299 (mtm-85) REVERT: D 62 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8166 (ttp-170) REVERT: E 12 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7838 (tt) REVERT: F 12 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7887 (tt) REVERT: F 117 GLN cc_start: 0.8795 (pt0) cc_final: 0.8446 (pt0) REVERT: I 35 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: I 53 ASP cc_start: 0.8681 (p0) cc_final: 0.8439 (p0) outliers start: 48 outliers final: 39 residues processed: 170 average time/residue: 1.0186 time to fit residues: 187.1434 Evaluate side-chains 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 29 MET 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.0010 chunk 72 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.4866 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.088951 restraints weight = 10655.558| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.38 r_work: 0.3139 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4195 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= 0.128 Angle : 0.688 9.435 12780 Z= 0.366 Chirality : 0.049 0.176 1305 Planarity : 0.003 0.052 1674 Dihedral : 6.869 30.318 1350 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.91 % Allowed : 25.21 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (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 TRP 0.014 0.002 TRP D 28 HIS 0.001 0.000 HIS B 78 PHE 0.011 0.002 PHE D 3 TYR 0.013 0.001 TYR B 124 ARG 0.014 0.000 ARG H 10 Details of bonding type rmsd hydrogen bonds : bond 0.06074 ( 96) hydrogen bonds : angle 5.57270 ( 288) SS BOND : bond 0.00314 ( 36) SS BOND : angle 0.54057 ( 72) covalent geometry : bond 0.00276 ( 9405) covalent geometry : angle 0.68833 (12708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6108.96 seconds wall clock time: 106 minutes 36.35 seconds (6396.35 seconds total)