Starting phenix.real_space_refine on Thu Jan 16 05:55:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r4a_18883/01_2025/8r4a_18883.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r4a_18883/01_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_18883/01_2025/8r4a_18883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r4a_18883/01_2025/8r4a_18883.map" model { file = "/net/cci-nas-00/data/ceres_data/8r4a_18883/01_2025/8r4a_18883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r4a_18883/01_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-5571/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: 5.57, per 1000 atoms: 0.60 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: 2.06 Conformation dependent library (CDL) restraints added in 987.7 milliseconds 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: 1.36 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: 2.59 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1503 1.30 - 1.43: 2718 1.43 - 1.56: 5076 1.56 - 1.69: 0 1.69 - 1.82: 108 Bond restraints: 9405 Sorted by residual: bond pdb=" C CYS D 6 " pdb=" O CYS D 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.69e+01 bond pdb=" C CYS I 6 " pdb=" O CYS I 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.69e+01 bond pdb=" C CYS F 6 " pdb=" O CYS F 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.69e+01 bond pdb=" C CYS G 6 " pdb=" O CYS G 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.68e+01 bond pdb=" C CYS E 6 " pdb=" O CYS E 6 " ideal model delta sigma weight residual 1.235 1.171 0.064 1.23e-02 6.61e+03 2.68e+01 ... (remaining 9400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 8771 1.87 - 3.75: 2561 3.75 - 5.62: 1160 5.62 - 7.50: 180 7.50 - 9.37: 36 Bond angle restraints: 12708 Sorted by residual: angle pdb=" CA ASP H 102 " pdb=" C ASP H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 118.16 122.86 -4.70 7.00e-01 2.04e+00 4.50e+01 angle pdb=" CA ASP F 102 " pdb=" C ASP F 102 " pdb=" N PRO F 103 " ideal model delta sigma weight residual 118.16 122.84 -4.68 7.00e-01 2.04e+00 4.47e+01 angle pdb=" CA ASP A 102 " pdb=" C ASP A 102 " pdb=" N PRO A 103 " ideal model delta sigma weight residual 118.16 122.82 -4.66 7.00e-01 2.04e+00 4.43e+01 angle pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 118.16 122.82 -4.66 7.00e-01 2.04e+00 4.43e+01 angle pdb=" CA ASP C 102 " pdb=" C ASP C 102 " pdb=" N PRO C 103 " ideal model delta sigma weight residual 118.16 122.81 -4.65 7.00e-01 2.04e+00 4.42e+01 ... (remaining 12703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 5067 15.61 - 31.22: 396 31.22 - 46.83: 117 46.83 - 62.43: 45 62.43 - 78.04: 36 Dihedral angle restraints: 5661 sinusoidal: 2322 harmonic: 3339 Sorted by residual: dihedral pdb=" CA ASN F 60 " pdb=" CB ASN F 60 " pdb=" CG ASN F 60 " pdb=" OD1 ASN F 60 " ideal model delta sinusoidal sigma weight residual -90.00 -159.22 69.22 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASN G 60 " pdb=" CB ASN G 60 " pdb=" CG ASN G 60 " pdb=" OD1 ASN G 60 " ideal model delta sinusoidal sigma weight residual -90.00 -159.22 69.22 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASN C 60 " pdb=" CB ASN C 60 " pdb=" CG ASN C 60 " pdb=" OD1 ASN C 60 " ideal model delta sinusoidal sigma weight residual -90.00 -159.21 69.21 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 5658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 561 0.064 - 0.128: 440 0.128 - 0.192: 205 0.192 - 0.256: 90 0.256 - 0.320: 9 Chirality restraints: 1305 Sorted by residual: chirality pdb=" CA VAL C 121 " pdb=" N VAL C 121 " pdb=" C VAL C 121 " pdb=" CB VAL C 121 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL F 121 " pdb=" N VAL F 121 " pdb=" C VAL F 121 " pdb=" CB VAL F 121 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL B 121 " pdb=" N VAL B 121 " pdb=" C VAL B 121 " pdb=" CB VAL B 121 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1302 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 31 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU C 31 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU C 31 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA C 32 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 31 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU I 31 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU I 31 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA I 32 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 31 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU B 31 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU B 31 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B 32 " 0.022 2.00e-02 2.50e+03 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3880 2.94 - 3.43: 9783 3.43 - 3.92: 16519 3.92 - 4.41: 20132 4.41 - 4.90: 35789 Nonbonded interactions: 86103 Sorted by model distance: nonbonded pdb=" N ASN G 118 " pdb=" O ASN G 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN E 118 " pdb=" O ASN E 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN H 118 " pdb=" O ASN H 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN A 118 " pdb=" O ASN A 118 " model vdw 2.451 2.496 nonbonded pdb=" N ASN B 118 " pdb=" O ASN B 118 " model vdw 2.451 2.496 ... (remaining 86098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.060 ------------------------------------------------------------------------------- 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 : 1.057 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: 1.2929 time to fit residues: 411.9815 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 58 GLN B 44 ASN B 58 GLN B 104 GLN C 44 ASN C 58 GLN C 88 ASN D 27 ASN D 44 ASN D 58 GLN E 44 ASN E 58 GLN ** E 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN F 44 ASN ** F 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 ASN H 44 ASN H 58 GLN ** H 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN I 44 ASN I 104 GLN I 114 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.112223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095056 restraints weight = 10774.801| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.31 r_work: 0.3230 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 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 : 1.074 Fit side-chains REVERT: B 12 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7440 (tt) REVERT: B 67 ASP cc_start: 0.8232 (t0) cc_final: 0.8008 (t0) REVERT: C 12 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7572 (tt) REVERT: C 62 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7806 (ttm170) REVERT: C 98 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7703 (ttm170) REVERT: C 106 ILE cc_start: 0.8658 (mp) cc_final: 0.8431 (mt) REVERT: C 113 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8067 (mtm-85) REVERT: D 29 MET cc_start: 0.8119 (mtt) cc_final: 0.7876 (mtt) REVERT: D 113 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: E 12 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7689 (tt) REVERT: E 98 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7890 (ttm170) REVERT: F 117 GLN cc_start: 0.8569 (pt0) cc_final: 0.8265 (pt0) REVERT: I 115 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (ttt90) outliers start: 54 outliers final: 19 residues processed: 206 average time/residue: 0.9998 time to fit residues: 223.2352 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 : 0.966 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.6298 ------------------------------------------------------------------------------- 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 G 88 ASN H 88 ASN H 114 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091632 restraints weight = 10891.631| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.37 r_work: 0.3175 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9405 Z= 0.230 Angle : 0.744 9.364 12708 Z= 0.399 Chirality : 0.049 0.176 1305 Planarity : 0.003 0.030 1674 Dihedral : 7.058 37.722 1350 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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 0.019 0.003 PHE F 3 TYR 0.011 0.002 TYR A 54 ARG 0.008 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 210 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 1.003 Fit side-chains REVERT: A 45 TYR cc_start: 0.9229 (m-80) cc_final: 0.9027 (m-80) REVERT: B 12 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7524 (tt) REVERT: B 67 ASP cc_start: 0.8219 (t0) cc_final: 0.8016 (t0) REVERT: C 12 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7724 (tt) REVERT: C 62 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7926 (ttp80) REVERT: C 98 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7877 (ttm170) REVERT: C 113 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8247 (mtm-85) REVERT: D 29 MET cc_start: 0.8204 (mtt) cc_final: 0.7969 (mtt) REVERT: D 62 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8125 (ttp-170) REVERT: E 12 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7742 (tt) REVERT: F 117 GLN cc_start: 0.8603 (pt0) cc_final: 0.8202 (pt0) REVERT: H 12 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7777 (tt) REVERT: I 118 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7584 (t0) outliers start: 54 outliers final: 25 residues processed: 190 average time/residue: 1.1457 time to fit residues: 234.3818 Evaluate side-chains 180 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 1 optimal weight: 0.0050 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.8174 ------------------------------------------------------------------------------- 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 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 = 0.3518 r_free = 0.3518 target = 0.106667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.088664 restraints weight = 10790.719| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.34 r_work: 0.3135 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3318 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= 0.274 Angle : 0.744 8.676 12708 Z= 0.397 Chirality : 0.050 0.171 1305 Planarity : 0.004 0.030 1674 Dihedral : 7.046 35.784 1350 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.56 % Allowed : 23.08 % 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 0.013 0.002 TRP B 112 HIS 0.004 0.002 HIS G 78 PHE 0.016 0.003 PHE F 3 TYR 0.011 0.002 TYR C 54 ARG 0.009 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 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.046 Fit side-chains REVERT: A 35 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: B 12 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 17 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8665 (mtm) REVERT: B 67 ASP cc_start: 0.8338 (t0) cc_final: 0.8080 (t0) REVERT: C 12 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7790 (tt) REVERT: C 62 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: C 98 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7932 (ttm170) REVERT: C 113 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8297 (mtm-85) REVERT: D 62 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8075 (ttp-170) REVERT: E 12 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7772 (tt) REVERT: F 12 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7824 (tt) REVERT: F 117 GLN cc_start: 0.8634 (pt0) cc_final: 0.8320 (pt0) REVERT: H 12 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7828 (tt) outliers start: 52 outliers final: 25 residues processed: 184 average time/residue: 1.1065 time to fit residues: 219.1192 Evaluate side-chains 186 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 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: 2.9990 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: 1.9990 chunk 95 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 D 123 GLN E 78 HIS E 88 ASN G 78 HIS G 88 ASN H 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.104383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085532 restraints weight = 10536.379| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.38 r_work: 0.3065 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9405 Z= 0.417 Angle : 0.812 9.307 12708 Z= 0.433 Chirality : 0.052 0.181 1305 Planarity : 0.005 0.037 1674 Dihedral : 7.358 41.315 1350 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.20 % Allowed : 23.18 % 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: -4.34 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (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 F 54 ARG 0.009 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 204 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 1.050 Fit side-chains REVERT: A 29 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8250 (mmt) REVERT: A 35 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: B 12 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7675 (tt) REVERT: B 67 ASP cc_start: 0.8323 (t0) cc_final: 0.8075 (t0) REVERT: C 12 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7927 (tt) REVERT: C 62 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7861 (ttp80) REVERT: C 98 ARG cc_start: 0.8282 (ttm110) cc_final: 0.8024 (ttm170) REVERT: C 113 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8281 (mtm-85) REVERT: D 62 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8102 (ttp-170) REVERT: E 12 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7851 (tt) REVERT: E 97 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (ttpt) REVERT: F 12 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7963 (tt) REVERT: F 117 GLN cc_start: 0.8774 (pt0) cc_final: 0.8426 (pt0) REVERT: I 53 ASP cc_start: 0.8751 (p0) cc_final: 0.8438 (p0) REVERT: I 62 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7950 (ttt90) outliers start: 58 outliers final: 36 residues processed: 178 average time/residue: 1.1585 time to fit residues: 221.4292 Evaluate side-chains 189 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 80 SER 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 70 THR Chi-restraints excluded: chain F residue 97 LYS 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 25 LEU Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 130 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 78 HIS H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086367 restraints weight = 10795.562| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.37 r_work: 0.3081 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9405 Z= 0.330 Angle : 0.765 8.366 12708 Z= 0.409 Chirality : 0.051 0.183 1305 Planarity : 0.004 0.044 1674 Dihedral : 7.258 39.806 1350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.62 % Allowed : 22.22 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.16), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.12), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 112 HIS 0.003 0.001 HIS H 78 PHE 0.017 0.002 PHE G 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 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 1.013 Fit side-chains REVERT: A 29 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (mmt) REVERT: A 35 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: B 12 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 67 ASP cc_start: 0.8323 (t0) cc_final: 0.8023 (t0) REVERT: C 12 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7899 (tt) REVERT: C 62 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7846 (ttp80) REVERT: C 98 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7957 (ttm170) REVERT: C 113 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8285 (mtm-85) REVERT: D 62 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8144 (ttp-170) REVERT: E 12 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7806 (tt) REVERT: E 97 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8202 (ttpt) REVERT: F 12 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7906 (tt) REVERT: F 117 GLN cc_start: 0.8750 (pt0) cc_final: 0.8452 (pt0) REVERT: G 17 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8431 (mtp) REVERT: I 35 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: I 53 ASP cc_start: 0.8740 (p0) cc_final: 0.8451 (p0) REVERT: I 115 ARG cc_start: 0.8359 (ttt90) cc_final: 0.8141 (ttt90) outliers start: 62 outliers final: 38 residues processed: 186 average time/residue: 1.1409 time to fit residues: 229.2136 Evaluate side-chains 199 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 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 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 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 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 80 SER 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 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 17 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.087739 restraints weight = 10814.738| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.38 r_work: 0.3114 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: 0.8196 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9405 Z= 0.215 Angle : 0.709 8.651 12708 Z= 0.380 Chirality : 0.049 0.170 1305 Planarity : 0.003 0.045 1674 Dihedral : 7.007 34.772 1350 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.45 % Allowed : 23.50 % 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: -4.22 (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 0.013 0.002 TRP D 28 HIS 0.001 0.000 HIS H 78 PHE 0.014 0.002 PHE F 3 TYR 0.011 0.001 TYR B 124 ARG 0.014 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 204 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.996 Fit side-chains REVERT: A 29 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8165 (mmt) REVERT: A 35 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: B 12 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 67 ASP cc_start: 0.8302 (t0) cc_final: 0.7981 (t0) REVERT: C 12 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7825 (tt) REVERT: C 62 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7704 (ttp80) REVERT: C 98 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7977 (ttm170) REVERT: C 113 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8299 (mtm-85) REVERT: D 62 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8149 (ttp-170) REVERT: E 12 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7764 (tt) REVERT: F 12 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7874 (tt) REVERT: F 117 GLN cc_start: 0.8723 (pt0) cc_final: 0.8260 (pt0) REVERT: I 115 ARG cc_start: 0.8385 (ttt90) cc_final: 0.8110 (ttt90) outliers start: 51 outliers final: 35 residues processed: 181 average time/residue: 1.0575 time to fit residues: 206.6976 Evaluate side-chains 192 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 80 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 0.0470 chunk 113 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.108544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089942 restraints weight = 10794.357| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.40 r_work: 0.3158 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9405 Z= 0.151 Angle : 0.660 8.864 12708 Z= 0.353 Chirality : 0.048 0.163 1305 Planarity : 0.003 0.049 1674 Dihedral : 6.693 27.857 1350 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.06 % Allowed : 25.00 % 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 0.013 0.002 TRP D 28 HIS 0.001 0.000 HIS C 78 PHE 0.012 0.002 PHE D 3 TYR 0.012 0.001 TYR B 124 ARG 0.015 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 185 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.997 Fit side-chains REVERT: A 35 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: B 12 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7638 (tt) REVERT: C 12 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 98 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7824 (ttm170) REVERT: C 113 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8261 (mtm-85) REVERT: E 12 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7727 (tt) REVERT: E 17 MET cc_start: 0.8743 (mtp) cc_final: 0.8493 (mtp) REVERT: F 12 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7794 (tt) REVERT: F 117 GLN cc_start: 0.8603 (pt0) cc_final: 0.8139 (pt0) REVERT: I 35 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: I 115 ARG cc_start: 0.8322 (ttt90) cc_final: 0.8024 (ttt90) outliers start: 38 outliers final: 24 residues processed: 167 average time/residue: 1.0531 time to fit residues: 190.1319 Evaluate side-chains 177 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 80 SER 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.088669 restraints weight = 10666.352| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.37 r_work: 0.3134 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9405 Z= 0.216 Angle : 0.688 9.092 12708 Z= 0.367 Chirality : 0.048 0.167 1305 Planarity : 0.003 0.051 1674 Dihedral : 6.769 30.368 1350 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.49 % Allowed : 24.25 % 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 : -3.23 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 112 HIS 0.002 0.001 HIS C 78 PHE 0.013 0.002 PHE G 3 TYR 0.015 0.001 TYR B 124 ARG 0.013 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 187 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.969 Fit side-chains REVERT: A 29 MET cc_start: 0.8440 (mmt) cc_final: 0.8073 (mtt) REVERT: A 35 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: B 12 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7699 (tt) REVERT: C 12 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7804 (tt) REVERT: C 98 ARG cc_start: 0.8197 (ttm110) cc_final: 0.7806 (ttm170) REVERT: C 113 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8257 (mtm-85) REVERT: D 62 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8145 (ttp-170) REVERT: E 12 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7764 (tt) REVERT: E 17 MET cc_start: 0.8691 (mtp) cc_final: 0.8426 (mtp) REVERT: F 12 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7834 (tt) REVERT: F 117 GLN cc_start: 0.8619 (pt0) cc_final: 0.8185 (pt0) REVERT: I 35 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8151 (mp0) outliers start: 42 outliers final: 30 residues processed: 169 average time/residue: 1.0496 time to fit residues: 191.6671 Evaluate side-chains 182 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 62 ARG 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 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 80 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 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 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 2 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 86 GLN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.106409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.087675 restraints weight = 10846.919| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.42 r_work: 0.3115 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9405 Z= 0.250 Angle : 0.708 9.424 12708 Z= 0.378 Chirality : 0.049 0.185 1305 Planarity : 0.003 0.050 1674 Dihedral : 6.865 32.298 1350 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.70 % Allowed : 24.15 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 112 HIS 0.002 0.001 HIS I 78 PHE 0.013 0.002 PHE G 3 TYR 0.016 0.002 TYR B 124 ARG 0.013 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 197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.051 Fit side-chains REVERT: A 29 MET cc_start: 0.8434 (mmt) cc_final: 0.8103 (mtt) REVERT: A 35 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: B 12 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7700 (tt) REVERT: C 12 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7855 (tt) REVERT: C 62 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7707 (ttp80) REVERT: C 98 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7881 (ttm170) REVERT: C 113 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8257 (mtm-85) REVERT: D 62 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (ttp-170) REVERT: E 12 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7808 (tt) REVERT: E 17 MET cc_start: 0.8740 (mtp) cc_final: 0.8495 (mtp) REVERT: E 97 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8079 (ttpt) REVERT: F 12 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7849 (tt) REVERT: F 117 GLN cc_start: 0.8657 (pt0) cc_final: 0.8213 (pt0) REVERT: I 35 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8206 (mp0) outliers start: 44 outliers final: 33 residues processed: 178 average time/residue: 1.1022 time to fit residues: 211.5101 Evaluate side-chains 193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 SER 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 130 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 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 130 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 6 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 86 GLN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086519 restraints weight = 10783.286| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.38 r_work: 0.3095 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9405 Z= 0.313 Angle : 0.751 9.761 12708 Z= 0.399 Chirality : 0.050 0.194 1305 Planarity : 0.004 0.050 1674 Dihedral : 7.042 35.537 1350 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.91 % Allowed : 24.15 % 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: -4.32 (0.17), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.13), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 112 HIS 0.002 0.001 HIS C 78 PHE 0.012 0.002 PHE F 3 TYR 0.018 0.002 TYR B 124 ARG 0.014 0.000 ARG B 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6404.40 seconds wall clock time: 114 minutes 37.40 seconds (6877.40 seconds total)