Starting phenix.real_space_refine on Sat Dec 28 21:18:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4a_18883/12_2024/8r4a_18883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4a_18883/12_2024/8r4a_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_18883/12_2024/8r4a_18883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4a_18883/12_2024/8r4a_18883.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4a_18883/12_2024/8r4a_18883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4a_18883/12_2024/8r4a_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-5532/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: 5.97, 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: 2.64 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: 1.23 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: 2.47 Time building geometry restraints manager: 2.97 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.700 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- 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 : 1.105 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: 1.3067 time to fit residues: 416.4277 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 : 1.107 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 1.104 Fit side-chains REVERT: B 12 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7620 (tt) REVERT: B 67 ASP cc_start: 0.7936 (t0) cc_final: 0.7703 (t0) REVERT: C 12 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7732 (tt) REVERT: C 62 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6905 (ttm170) REVERT: C 98 ARG cc_start: 0.7346 (ttm110) cc_final: 0.6991 (ttm170) REVERT: C 113 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7331 (mtm-85) REVERT: D 113 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7422 (mtm-85) REVERT: E 12 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7870 (tt) REVERT: E 98 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7312 (ttm170) REVERT: F 117 GLN cc_start: 0.8477 (pt0) cc_final: 0.8188 (pt0) REVERT: I 115 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7294 (ttt90) outliers start: 54 outliers final: 19 residues processed: 206 average time/residue: 1.0196 time to fit residues: 227.8061 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 : 1.403 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 78 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN E 88 ASN F 88 ASN F 104 GLN ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 ASN H 88 ASN H 114 ASN I 78 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2990 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= 0.288 Angle : 0.780 9.709 12708 Z= 0.417 Chirality : 0.050 0.176 1305 Planarity : 0.003 0.026 1674 Dihedral : 7.315 41.663 1350 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.66 % Allowed : 22.33 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.15), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 207 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 1.133 Fit side-chains REVERT: B 12 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7794 (tt) REVERT: B 67 ASP cc_start: 0.7951 (t0) cc_final: 0.7741 (t0) REVERT: C 12 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7972 (tt) REVERT: C 62 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7098 (ttp80) REVERT: C 98 ARG cc_start: 0.7498 (ttm110) cc_final: 0.7188 (ttm170) REVERT: C 113 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7495 (mtm-85) REVERT: D 62 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7232 (ttp-170) REVERT: E 12 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8019 (tt) REVERT: F 117 GLN cc_start: 0.8587 (pt0) cc_final: 0.8231 (pt0) REVERT: I 118 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7365 (t0) outliers start: 53 outliers final: 25 residues processed: 190 average time/residue: 1.1320 time to fit residues: 231.6713 Evaluate side-chains 181 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 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 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 105 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 0.0170 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 ASN C 114 ASN D 78 HIS E 88 ASN F 78 HIS G 78 HIS G 88 ASN H 88 ASN H 104 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3444 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= 0.468 Angle : 0.856 10.039 12708 Z= 0.453 Chirality : 0.053 0.183 1305 Planarity : 0.005 0.032 1674 Dihedral : 7.559 45.389 1350 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 6.52 % Allowed : 22.76 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 112 HIS 0.006 0.002 HIS B 78 PHE 0.017 0.003 PHE F 3 TYR 0.014 0.002 TYR F 54 ARG 0.010 0.001 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 211 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 150 time to evaluate : 1.095 Fit side-chains REVERT: A 35 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: B 12 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7942 (tt) REVERT: B 67 ASP cc_start: 0.8114 (t0) cc_final: 0.7881 (t0) REVERT: C 12 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8137 (tt) REVERT: C 62 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6621 (ttm170) REVERT: C 98 ARG cc_start: 0.7564 (ttm110) cc_final: 0.7262 (ttm170) REVERT: C 113 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7530 (mtm-85) REVERT: D 62 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7230 (ttp-170) REVERT: E 12 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8030 (tt) REVERT: F 12 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8123 (tt) REVERT: H 12 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8219 (tt) REVERT: I 62 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7048 (ttt90) REVERT: I 115 ARG cc_start: 0.7617 (ttt90) cc_final: 0.7365 (ttt90) outliers start: 61 outliers final: 37 residues processed: 185 average time/residue: 1.2482 time to fit residues: 247.1836 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 74 VAL 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 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 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 12 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 86 GLN E 88 ASN H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9405 Z= 0.265 Angle : 0.744 8.186 12708 Z= 0.400 Chirality : 0.050 0.176 1305 Planarity : 0.004 0.038 1674 Dihedral : 7.239 39.891 1350 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.98 % Allowed : 22.97 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 28 HIS 0.004 0.001 HIS E 78 PHE 0.016 0.002 PHE G 3 TYR 0.011 0.002 TYR A 54 ARG 0.010 0.000 ARG B 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 205 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 149 time to evaluate : 1.088 Fit side-chains REVERT: A 35 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: B 12 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7947 (tt) REVERT: B 67 ASP cc_start: 0.8096 (t0) cc_final: 0.7775 (t0) REVERT: C 12 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8042 (tt) REVERT: C 62 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7005 (ttp80) REVERT: C 98 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7280 (ttm170) REVERT: C 113 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7548 (mtm-85) REVERT: D 62 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7262 (ttp-170) REVERT: E 12 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7934 (tt) REVERT: E 113 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7589 (mtm-85) REVERT: F 12 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8037 (tt) REVERT: F 117 GLN cc_start: 0.8656 (pt0) cc_final: 0.8323 (pt0) REVERT: I 35 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7425 (mp0) outliers start: 56 outliers final: 30 residues processed: 180 average time/residue: 1.1894 time to fit residues: 229.8176 Evaluate side-chains 188 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 18 ASP Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 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 74 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 113 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain H residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 78 HIS E 86 GLN H 78 HIS H 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9405 Z= 0.347 Angle : 0.774 8.664 12708 Z= 0.413 Chirality : 0.051 0.178 1305 Planarity : 0.004 0.035 1674 Dihedral : 7.292 39.926 1350 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.84 % Allowed : 21.90 % Favored : 71.26 % 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 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 112 HIS 0.005 0.001 HIS E 78 PHE 0.016 0.002 PHE G 3 TYR 0.012 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 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 1.052 Fit side-chains REVERT: A 29 MET cc_start: 0.7709 (mmt) cc_final: 0.7351 (mtt) REVERT: A 35 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7555 (mt-10) REVERT: B 12 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8011 (tt) REVERT: B 67 ASP cc_start: 0.8049 (t0) cc_final: 0.7748 (t0) REVERT: C 12 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8084 (tt) REVERT: C 62 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7012 (ttp80) REVERT: C 98 ARG cc_start: 0.7523 (ttm110) cc_final: 0.7200 (ttm170) REVERT: C 113 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7547 (mtm-85) REVERT: D 62 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7246 (ttp-170) REVERT: E 12 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8004 (tt) REVERT: E 113 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7559 (mtm-85) REVERT: F 12 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8063 (tt) REVERT: I 35 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7459 (mp0) outliers start: 64 outliers final: 42 residues processed: 182 average time/residue: 1.1412 time to fit residues: 224.2656 Evaluate side-chains 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 29 MET 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 120 ASP 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 113 ARG 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 59 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 86 GLN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3891 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= 0.246 Angle : 0.723 8.577 12708 Z= 0.388 Chirality : 0.050 0.174 1305 Planarity : 0.003 0.045 1674 Dihedral : 7.093 36.104 1350 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -4.25 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 28 HIS 0.001 0.001 HIS B 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 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.061 Fit side-chains REVERT: A 29 MET cc_start: 0.7633 (mmt) cc_final: 0.7348 (mtt) REVERT: A 35 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: B 12 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7994 (tt) REVERT: B 67 ASP cc_start: 0.8050 (t0) cc_final: 0.7728 (t0) REVERT: C 12 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8018 (tt) REVERT: C 62 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7001 (ttp80) REVERT: C 98 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7197 (ttm170) REVERT: C 113 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7512 (mtm-85) REVERT: D 62 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7268 (ttp-170) REVERT: E 12 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7947 (tt) REVERT: E 113 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7547 (mtm-85) REVERT: F 12 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8035 (tt) REVERT: F 117 GLN cc_start: 0.8668 (pt0) cc_final: 0.8363 (pt0) REVERT: I 35 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7453 (mp0) outliers start: 56 outliers final: 38 residues processed: 185 average time/residue: 1.1016 time to fit residues: 219.4289 Evaluate side-chains 201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 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 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 120 ASP 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 113 ARG Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN E 86 GLN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9405 Z= 0.385 Angle : 0.789 8.987 12708 Z= 0.419 Chirality : 0.051 0.187 1305 Planarity : 0.004 0.046 1674 Dihedral : 7.291 39.633 1350 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.09 % Allowed : 23.08 % 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: -4.30 (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 B 112 HIS 0.003 0.001 HIS B 78 PHE 0.015 0.002 PHE G 3 TYR 0.014 0.002 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 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 149 time to evaluate : 1.147 Fit side-chains REVERT: A 29 MET cc_start: 0.7668 (mmt) cc_final: 0.7359 (mtt) REVERT: A 35 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: B 12 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7942 (tt) REVERT: B 67 ASP cc_start: 0.8077 (t0) cc_final: 0.7769 (t0) REVERT: C 12 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8096 (tt) REVERT: C 62 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7020 (ttp80) REVERT: C 113 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7512 (mtm-85) REVERT: D 62 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7233 (ttp-170) REVERT: E 12 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8031 (tt) REVERT: E 113 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: F 12 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8101 (tt) REVERT: F 35 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: G 45 TYR cc_start: 0.8959 (m-80) cc_final: 0.8752 (m-80) REVERT: I 35 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: I 62 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7038 (ttt90) outliers start: 57 outliers final: 42 residues processed: 178 average time/residue: 1.0946 time to fit residues: 210.2244 Evaluate side-chains 200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 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 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 29 MET 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 120 ASP 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 113 ARG 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 35 GLU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 0.0060 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9405 Z= 0.362 Angle : 0.784 9.128 12708 Z= 0.417 Chirality : 0.051 0.205 1305 Planarity : 0.004 0.052 1674 Dihedral : 7.298 40.140 1350 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.88 % Allowed : 23.50 % 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: -4.33 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (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 0.014 0.002 PHE G 3 TYR 0.014 0.002 TYR B 124 ARG 0.015 0.000 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 205 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 150 time to evaluate : 1.097 Fit side-chains REVERT: A 29 MET cc_start: 0.7637 (mmt) cc_final: 0.7335 (mtt) REVERT: A 35 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 85 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8084 (pp) REVERT: B 12 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 67 ASP cc_start: 0.8086 (t0) cc_final: 0.7796 (t0) REVERT: C 12 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8108 (tt) REVERT: C 62 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7013 (ttp80) REVERT: C 113 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7511 (mtm-85) REVERT: D 62 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7238 (ttp-170) REVERT: E 12 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8009 (tt) REVERT: E 113 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7552 (mtm-85) REVERT: F 12 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8083 (tt) REVERT: F 35 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: I 35 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7480 (mp0) outliers start: 55 outliers final: 42 residues processed: 177 average time/residue: 1.0414 time to fit residues: 199.3176 Evaluate side-chains 199 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 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 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 29 MET 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 120 ASP 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 113 ARG 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 35 GLU 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 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 59 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN I 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4118 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= 0.465 Angle : 0.842 9.558 12708 Z= 0.446 Chirality : 0.053 0.215 1305 Planarity : 0.005 0.047 1674 Dihedral : 7.524 44.038 1350 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.98 % Allowed : 23.72 % 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: -4.36 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 112 HIS 0.004 0.001 HIS G 78 PHE 0.014 0.002 PHE H 3 TYR 0.016 0.002 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 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 1.083 Fit side-chains REVERT: A 29 MET cc_start: 0.7698 (mmt) cc_final: 0.7378 (mtt) REVERT: A 35 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: B 12 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8009 (tt) REVERT: B 67 ASP cc_start: 0.8095 (t0) cc_final: 0.7814 (t0) REVERT: C 12 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8133 (tt) REVERT: C 62 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6617 (ttm170) REVERT: C 113 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7574 (mtm-85) REVERT: D 62 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7205 (ttp-170) REVERT: E 12 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8075 (tt) REVERT: E 113 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7558 (mtm-85) REVERT: F 12 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8112 (tt) REVERT: F 35 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: I 35 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: I 53 ASP cc_start: 0.8224 (p0) cc_final: 0.7979 (p0) REVERT: I 62 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7015 (ttt90) outliers start: 56 outliers final: 44 residues processed: 181 average time/residue: 1.1237 time to fit residues: 220.0819 Evaluate side-chains 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 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 11 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 29 MET 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 120 ASP 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 113 ARG 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 35 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086317 restraints weight = 10467.469| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.37 r_work: 0.3078 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9405 Z= 0.283 Angle : 0.753 9.105 12708 Z= 0.403 Chirality : 0.050 0.192 1305 Planarity : 0.004 0.055 1674 Dihedral : 7.262 38.219 1350 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.77 % Allowed : 24.25 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.36 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 112 HIS 0.002 0.001 HIS C 78 PHE 0.012 0.002 PHE D 3 TYR 0.014 0.002 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: 4055.37 seconds wall clock time: 73 minutes 27.36 seconds (4407.36 seconds total)