Starting phenix.real_space_refine on Thu Mar 13 18:58:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4a_18883/03_2025/8r4a_18883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4a_18883/03_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_18883/03_2025/8r4a_18883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4a_18883/03_2025/8r4a_18883.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4a_18883/03_2025/8r4a_18883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4a_18883/03_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-5624/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: 6.02, 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: 2.24 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 2.45 Time building geometry restraints manager: 2.71 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: 0.07 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: 1.820 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.130 Find NCS groups from input model: 0.170 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.870 ------------------------------------------------------------------------------- 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 9405 Z= 0.887 Angle : 2.163 9.371 12708 Z= 1.565 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 *********************** 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 : 1.560 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: 1.4036 time to fit residues: 446.5115 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 : 0.987 ------------------------------------------------------------------------------- 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 = 40)----------------| | 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: 0.3229 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 9405 Z= 0.292 Angle : 0.835 9.993 12708 Z= 0.452 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 *********************** 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 : 0.986 Fit side-chains REVERT: B 12 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7448 (tt) REVERT: B 67 ASP cc_start: 0.8230 (t0) cc_final: 0.8007 (t0) REVERT: C 12 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7581 (tt) REVERT: C 62 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7805 (ttm170) REVERT: C 98 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7718 (ttm170) REVERT: C 106 ILE cc_start: 0.8661 (mp) cc_final: 0.8433 (mt) REVERT: C 113 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8071 (mtm-85) REVERT: D 29 MET cc_start: 0.8119 (mtt) cc_final: 0.7877 (mtt) REVERT: D 113 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8245 (mtm-85) REVERT: E 12 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7698 (tt) REVERT: E 98 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7893 (ttm170) REVERT: F 117 GLN cc_start: 0.8565 (pt0) cc_final: 0.8262 (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: 0.9896 time to fit residues: 221.8761 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 : 1.025 ------------------------------------------------------------------------------- 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: 0.0770 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN F 88 ASN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 ASN H 88 ASN H 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091582 restraints weight = 10888.357| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.37 r_work: 0.3175 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9405 Z= 0.227 Angle : 0.743 9.388 12708 Z= 0.399 Chirality : 0.049 0.173 1305 Planarity : 0.003 0.030 1674 Dihedral : 7.048 37.537 1350 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.77 % Allowed : 21.90 % Favored : 72.33 % 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 : -3.22 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 112 HIS 0.004 0.002 HIS B 78 PHE 0.018 0.003 PHE F 3 TYR 0.012 0.002 TYR A 54 ARG 0.009 0.000 ARG H 10 *********************** 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 211 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 1.091 Fit side-chains REVERT: A 45 TYR cc_start: 0.9232 (m-80) cc_final: 0.9031 (m-80) REVERT: B 12 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7523 (tt) REVERT: B 67 ASP cc_start: 0.8222 (t0) cc_final: 0.8020 (t0) REVERT: C 12 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7725 (tt) REVERT: C 62 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7919 (ttp80) REVERT: C 98 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7875 (ttm170) REVERT: C 113 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: D 29 MET cc_start: 0.8206 (mtt) cc_final: 0.7974 (mtt) REVERT: D 62 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8125 (ttp-170) REVERT: E 12 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7740 (tt) REVERT: F 117 GLN cc_start: 0.8604 (pt0) cc_final: 0.8202 (pt0) REVERT: H 12 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7776 (tt) REVERT: I 118 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7583 (t0) outliers start: 54 outliers final: 25 residues processed: 191 average time/residue: 1.4642 time to fit residues: 301.6862 Evaluate side-chains 181 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 25 LEU 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 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: 3.9990 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 88 ASN C 114 ASN E 88 ASN F 78 HIS ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 ASN H 88 ASN H 104 GLN I 78 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087650 restraints weight = 10812.035| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.31 r_work: 0.3114 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9405 Z= 0.319 Angle : 0.775 9.083 12708 Z= 0.413 Chirality : 0.051 0.171 1305 Planarity : 0.004 0.036 1674 Dihedral : 7.176 37.815 1350 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.98 % Allowed : 22.65 % Favored : 71.37 % 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 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 112 HIS 0.005 0.002 HIS E 78 PHE 0.017 0.003 PHE F 3 TYR 0.013 0.002 TYR C 54 ARG 0.008 0.000 ARG H 10 *********************** 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 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.014 Fit side-chains REVERT: A 35 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: A 86 GLN cc_start: 0.8910 (tt0) cc_final: 0.8708 (tt0) REVERT: B 12 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7694 (tt) REVERT: B 17 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8653 (mtm) REVERT: B 67 ASP cc_start: 0.8352 (t0) cc_final: 0.8135 (t0) REVERT: C 12 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7847 (tt) REVERT: C 62 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7854 (ttp80) REVERT: C 98 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7960 (ttm170) REVERT: C 113 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8287 (mtm-85) REVERT: D 62 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (ttp-170) REVERT: E 12 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7773 (tt) REVERT: E 97 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: F 12 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7891 (tt) REVERT: F 117 GLN cc_start: 0.8670 (pt0) cc_final: 0.8360 (pt0) REVERT: H 12 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7883 (tt) outliers start: 56 outliers final: 26 residues processed: 183 average time/residue: 1.1069 time to fit residues: 217.8924 Evaluate side-chains 185 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 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 97 LYS 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 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** D 78 HIS E 78 HIS E 88 ASN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 HIS G 88 ASN H 78 HIS H 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.103454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084629 restraints weight = 10529.039| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.37 r_work: 0.3051 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9405 Z= 0.472 Angle : 0.838 9.742 12708 Z= 0.447 Chirality : 0.053 0.186 1305 Planarity : 0.005 0.037 1674 Dihedral : 7.503 44.756 1350 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.94 % Allowed : 22.44 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.32 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 112 HIS 0.006 0.002 HIS E 78 PHE 0.018 0.003 PHE G 3 TYR 0.014 0.002 TYR F 54 ARG 0.011 0.000 ARG H 10 *********************** 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 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 149 time to evaluate : 1.493 Fit side-chains REVERT: A 29 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8248 (mmt) REVERT: A 35 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: B 12 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7692 (tt) REVERT: B 67 ASP cc_start: 0.8298 (t0) cc_final: 0.8066 (t0) REVERT: C 12 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7972 (tt) REVERT: C 62 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7495 (ttm170) REVERT: C 98 ARG cc_start: 0.8296 (ttm110) cc_final: 0.8036 (ttm170) REVERT: C 113 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (mtm-85) REVERT: D 62 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8099 (ttp-170) REVERT: E 12 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7886 (tt) REVERT: E 97 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8313 (ttpt) REVERT: F 12 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7983 (tt) REVERT: I 53 ASP cc_start: 0.8741 (p0) cc_final: 0.8439 (p0) REVERT: I 62 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7878 (ttt90) outliers start: 65 outliers final: 39 residues processed: 184 average time/residue: 1.2414 time to fit residues: 244.3452 Evaluate side-chains 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 18 ASP 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 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 97 LYS Chi-restraints excluded: chain E residue 118 ASN 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 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 130 VAL Chi-restraints excluded: chain I residue 11 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** 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 = 0.3483 r_free = 0.3483 target = 0.104538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085941 restraints weight = 10790.842| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.40 r_work: 0.3076 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9405 Z= 0.328 Angle : 0.770 8.432 12708 Z= 0.411 Chirality : 0.051 0.184 1305 Planarity : 0.004 0.040 1674 Dihedral : 7.314 41.098 1350 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.20 % Allowed : 22.86 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -3.21 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 112 HIS 0.002 0.001 HIS B 78 PHE 0.016 0.002 PHE F 3 TYR 0.011 0.002 TYR B 124 ARG 0.013 0.000 ARG H 10 *********************** 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 209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 1.013 Fit side-chains REVERT: A 29 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8213 (mmt) REVERT: A 35 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: A 85 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8148 (pp) REVERT: B 12 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7630 (tt) REVERT: B 67 ASP cc_start: 0.8334 (t0) cc_final: 0.8014 (t0) REVERT: C 12 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7892 (tt) REVERT: C 62 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: C 98 ARG cc_start: 0.8299 (ttm110) cc_final: 0.8001 (ttm170) REVERT: C 113 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8328 (mtm-85) REVERT: D 62 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8126 (ttp-170) REVERT: E 12 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7811 (tt) REVERT: F 12 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7916 (tt) REVERT: I 53 ASP cc_start: 0.8746 (p0) cc_final: 0.8467 (p0) REVERT: I 115 ARG cc_start: 0.8334 (ttt90) cc_final: 0.8112 (ttt90) outliers start: 58 outliers final: 37 residues processed: 182 average time/residue: 1.0606 time to fit residues: 208.8669 Evaluate side-chains 192 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 18 ASP 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 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU 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 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 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 86 GLN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086054 restraints weight = 10879.996| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.42 r_work: 0.3083 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9405 Z= 0.293 Angle : 0.748 8.343 12708 Z= 0.400 Chirality : 0.050 0.179 1305 Planarity : 0.004 0.046 1674 Dihedral : 7.200 38.325 1350 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.88 % Allowed : 23.18 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.22 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 112 HIS 0.002 0.001 HIS C 78 PHE 0.014 0.002 PHE G 3 TYR 0.012 0.002 TYR B 124 ARG 0.013 0.000 ARG H 10 *********************** 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 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.052 Fit side-chains REVERT: A 29 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8226 (mmt) REVERT: A 35 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: B 12 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7700 (tt) REVERT: B 67 ASP cc_start: 0.8316 (t0) cc_final: 0.7981 (t0) REVERT: C 12 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7890 (tt) REVERT: C 62 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7865 (ttp80) REVERT: C 98 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7948 (ttm170) REVERT: C 113 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8286 (mtm-85) REVERT: D 62 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8127 (ttp-170) REVERT: E 12 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7824 (tt) REVERT: F 12 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7909 (tt) REVERT: F 117 GLN cc_start: 0.8814 (pt0) cc_final: 0.8461 (pt0) REVERT: H 17 MET cc_start: 0.8730 (mtm) cc_final: 0.8472 (mtm) REVERT: I 35 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: I 53 ASP cc_start: 0.8755 (p0) cc_final: 0.8496 (p0) REVERT: I 115 ARG cc_start: 0.8397 (ttt90) cc_final: 0.8122 (ttt90) outliers start: 55 outliers final: 38 residues processed: 184 average time/residue: 0.9880 time to fit residues: 197.2486 Evaluate side-chains 202 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 154 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 18 ASP 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 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 2.9990 chunk 113 optimal weight: 0.0060 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 0.0470 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 0.4294 ------------------------------------------------------------------------------- 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 E 104 GLN ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.088682 restraints weight = 10859.750| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.40 r_work: 0.3134 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9405 Z= 0.176 Angle : 0.680 8.865 12708 Z= 0.365 Chirality : 0.048 0.169 1305 Planarity : 0.003 0.049 1674 Dihedral : 6.867 31.113 1350 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.81 % Allowed : 24.36 % Favored : 70.83 % 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: -4.22 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (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 C 78 PHE 0.013 0.002 PHE D 3 TYR 0.012 0.001 TYR B 124 ARG 0.013 0.000 ARG H 10 *********************** 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 202 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.985 Fit side-chains REVERT: A 29 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8144 (mmt) REVERT: A 35 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: B 12 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 17 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8574 (mtm) REVERT: C 12 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7801 (tt) REVERT: C 62 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7702 (ttp80) REVERT: C 98 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7830 (ttm170) REVERT: C 113 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8276 (mtm-85) REVERT: D 62 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8161 (ttp-170) REVERT: E 12 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7798 (tt) REVERT: E 17 MET cc_start: 0.8750 (mtp) cc_final: 0.8488 (mtp) REVERT: F 12 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7813 (tt) REVERT: F 117 GLN cc_start: 0.8704 (pt0) cc_final: 0.8173 (pt0) REVERT: H 17 MET cc_start: 0.8713 (mtm) cc_final: 0.8465 (mtm) REVERT: I 35 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: I 115 ARG cc_start: 0.8294 (ttt90) cc_final: 0.7997 (ttt90) outliers start: 45 outliers final: 28 residues processed: 182 average time/residue: 1.0379 time to fit residues: 203.7601 Evaluate side-chains 190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 35 GLU Chi-restraints excluded: chain I residue 52 THR 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: 3.9990 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 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 = 0.3455 r_free = 0.3455 target = 0.103053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084110 restraints weight = 10522.193| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.37 r_work: 0.3052 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 9405 Z= 0.478 Angle : 0.832 9.594 12708 Z= 0.441 Chirality : 0.053 0.205 1305 Planarity : 0.005 0.047 1674 Dihedral : 7.355 40.598 1350 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.45 % Allowed : 23.72 % Favored : 70.83 % 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: -4.29 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 112 HIS 0.003 0.001 HIS B 78 PHE 0.016 0.003 PHE G 3 TYR 0.015 0.002 TYR B 124 ARG 0.015 0.001 ARG H 10 *********************** 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 201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.042 Fit side-chains REVERT: A 29 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8223 (mmt) REVERT: A 35 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: B 12 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7751 (tt) REVERT: B 17 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8567 (mtm) REVERT: B 67 ASP cc_start: 0.8328 (t0) cc_final: 0.7997 (t0) REVERT: C 12 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7985 (tt) REVERT: C 62 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7908 (ttp80) REVERT: C 113 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8305 (mtm-85) REVERT: D 62 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8131 (ttp-170) REVERT: E 12 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7925 (tt) REVERT: E 17 MET cc_start: 0.8712 (mtp) cc_final: 0.8472 (mtp) REVERT: E 97 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8308 (ttpt) REVERT: F 12 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7997 (tt) REVERT: I 35 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: I 53 ASP cc_start: 0.8729 (p0) cc_final: 0.8484 (p0) REVERT: I 62 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7892 (ttt90) outliers start: 51 outliers final: 34 residues processed: 179 average time/residue: 0.9928 time to fit residues: 192.3337 Evaluate side-chains 193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET 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 79 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 100 VAL 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 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 70 THR 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 62 ARG Chi-restraints excluded: chain I residue 70 THR 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: 0.5980 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 I 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.087554 restraints weight = 10787.001| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.38 r_work: 0.3113 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9405 Z= 0.214 Angle : 0.713 9.226 12708 Z= 0.382 Chirality : 0.049 0.189 1305 Planarity : 0.004 0.054 1674 Dihedral : 7.028 34.355 1350 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.70 % Allowed : 25.00 % 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: -4.31 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 28 HIS 0.001 0.001 HIS F 78 PHE 0.012 0.002 PHE D 3 TYR 0.014 0.001 TYR B 124 ARG 0.014 0.000 ARG H 10 ********************** 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 190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.631 Fit side-chains REVERT: A 29 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8176 (mmt) REVERT: A 35 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: B 12 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7714 (tt) REVERT: B 17 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8582 (mtm) REVERT: C 12 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7893 (tt) REVERT: C 62 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7696 (ttp80) REVERT: C 113 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8258 (mtm-85) REVERT: D 62 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8181 (ttp-170) REVERT: E 12 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7821 (tt) REVERT: E 17 MET cc_start: 0.8717 (mtp) cc_final: 0.8482 (mtp) REVERT: F 12 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7868 (tt) REVERT: F 117 GLN cc_start: 0.8763 (pt0) cc_final: 0.8402 (pt0) REVERT: I 35 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8197 (mp0) outliers start: 44 outliers final: 33 residues processed: 169 average time/residue: 1.1998 time to fit residues: 219.0208 Evaluate side-chains 187 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 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 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 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.0000 chunk 72 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 63 optimal weight: 0.0870 overall best weight: 0.2480 ------------------------------------------------------------------------------- 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 G 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 = 0.3566 r_free = 0.3566 target = 0.110043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.091155 restraints weight = 10486.282| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.41 r_work: 0.3167 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9405 Z= 0.147 Angle : 0.652 9.414 12708 Z= 0.347 Chirality : 0.048 0.165 1305 Planarity : 0.003 0.057 1674 Dihedral : 6.643 25.895 1350 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.06 % Allowed : 25.64 % 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: -4.26 (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 0.015 0.002 TRP D 28 HIS 0.001 0.000 HIS H 78 PHE 0.011 0.002 PHE D 3 TYR 0.013 0.001 TYR B 124 ARG 0.016 0.000 ARG H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7096.99 seconds wall clock time: 125 minutes 19.84 seconds (7519.84 seconds total)