Starting phenix.real_space_refine on Sat Oct 24 13:29:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/38ky_78897/10_2026/38ky_78897.cif Found real_map, /net/cci-nas-00/data/ceres_data/38ky_78897/10_2026/38ky_78897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/38ky_78897/10_2026/38ky_78897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/38ky_78897/10_2026/38ky_78897.map" model { file = "/net/cci-nas-00/data/ceres_data/38ky_78897/10_2026/38ky_78897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/38ky_78897/10_2026/38ky_78897.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 40 5.16 5 C 8530 2.51 5 N 2230 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13270 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "B" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "C" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "G" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "H" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "I" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Chain: "J" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 6, 'TRANS': 160} Time building chain proxies: 2.96, per 1000 atoms: 0.22 Number of scatterers: 13270 At special positions: 0 Unit cell: (142.78, 138.06, 60.18, 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 40 16.00 O 2470 8.00 N 2230 7.00 C 8530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.05 Conformation dependent library (CDL) restraints added in 633.3 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 15 sheets defined 35.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.957A pdb=" N GLY A 53 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.775A pdb=" N VAL A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.951A pdb=" N GLY B 53 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 91 through 98 Processing helix chain 'B' and resid 109 through 119 Processing helix chain 'B' and resid 140 through 146 Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.803A pdb=" N VAL B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.945A pdb=" N GLY C 53 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 140 through 146 Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.783A pdb=" N VAL C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.985A pdb=" N GLY D 53 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 140 through 146 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.795A pdb=" N VAL D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.943A pdb=" N GLY E 53 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.777A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.946A pdb=" N GLY F 53 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'F' and resid 109 through 119 Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.779A pdb=" N VAL F 185 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.968A pdb=" N GLY G 53 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.792A pdb=" N VAL G 185 " --> pdb=" O ASN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 54 removed outlier: 3.945A pdb=" N GLY H 53 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 91 through 98 Processing helix chain 'H' and resid 109 through 119 Processing helix chain 'H' and resid 140 through 146 Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.783A pdb=" N VAL H 185 " --> pdb=" O ASN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 54 removed outlier: 3.951A pdb=" N GLY I 53 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 91 through 98 Processing helix chain 'I' and resid 109 through 119 Processing helix chain 'I' and resid 140 through 146 Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.803A pdb=" N VAL I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 54 removed outlier: 3.962A pdb=" N GLY J 53 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 91 through 98 Processing helix chain 'J' and resid 109 through 119 Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.774A pdb=" N VAL J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.620A pdb=" N TYR A 67 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 103 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL A 69 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL A 105 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE A 71 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 170 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B 170 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR B 67 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE B 103 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 69 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 105 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 71 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.613A pdb=" N TYR C 67 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE C 103 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL C 69 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 105 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE C 71 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS C 170 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 170 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR D 67 " --> pdb=" O GLN D 101 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE D 103 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 69 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL D 105 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE D 71 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AA7, first strand: chain 'E' and resid 46 through 48 Processing sheet with id=AA8, first strand: chain 'E' and resid 100 through 105 removed outlier: 3.626A pdb=" N HIS E 170 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS F 170 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 46 through 48 Processing sheet with id=AB1, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AB2, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.639A pdb=" N TYR G 67 " --> pdb=" O GLN G 101 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE G 103 " --> pdb=" O TYR G 67 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL G 69 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL G 105 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE G 71 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS G 170 " --> pdb=" O VAL G 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS H 170 " --> pdb=" O VAL H 161 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR H 67 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE H 103 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 69 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL H 105 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE H 71 " --> pdb=" O VAL H 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 46 through 48 Processing sheet with id=AB4, first strand: chain 'I' and resid 46 through 48 Processing sheet with id=AB5, first strand: chain 'I' and resid 100 through 105 removed outlier: 6.645A pdb=" N TYR I 67 " --> pdb=" O GLN I 101 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE I 103 " --> pdb=" O TYR I 67 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL I 69 " --> pdb=" O ILE I 103 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL I 105 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE I 71 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS I 170 " --> pdb=" O VAL I 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS J 170 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR J 67 " --> pdb=" O GLN J 101 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE J 103 " --> pdb=" O TYR J 67 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL J 69 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL J 105 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE J 71 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 46 through 48 480 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4318 1.34 - 1.46: 3004 1.46 - 1.58: 6188 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 13570 Sorted by residual: bond pdb=" CB PRO B 74 " pdb=" CG PRO B 74 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.21e-01 bond pdb=" CB PRO G 74 " pdb=" CG PRO G 74 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.84e-01 bond pdb=" CB PRO I 74 " pdb=" CG PRO I 74 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.82e-01 bond pdb=" CB PRO D 74 " pdb=" CG PRO D 74 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.67e-01 bond pdb=" CB PRO E 74 " pdb=" CG PRO E 74 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.41e-01 ... (remaining 13565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 17463 1.13 - 2.27: 738 2.27 - 3.40: 128 3.40 - 4.53: 27 4.53 - 5.67: 14 Bond angle restraints: 18370 Sorted by residual: angle pdb=" CA LYS J 122 " pdb=" CB LYS J 122 " pdb=" CG LYS J 122 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.80e+00 angle pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " pdb=" CG LYS A 122 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.45e+00 angle pdb=" N PHE H 79 " pdb=" CA PHE H 79 " pdb=" C PHE H 79 " ideal model delta sigma weight residual 113.23 110.10 3.13 1.22e+00 6.72e-01 6.59e+00 angle pdb=" CB LYS J 122 " pdb=" CG LYS J 122 " pdb=" CD LYS J 122 " ideal model delta sigma weight residual 111.30 116.97 -5.67 2.30e+00 1.89e-01 6.07e+00 angle pdb=" CB LYS A 122 " pdb=" CG LYS A 122 " pdb=" CD LYS A 122 " ideal model delta sigma weight residual 111.30 116.73 -5.43 2.30e+00 1.89e-01 5.58e+00 ... (remaining 18365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 6839 16.31 - 32.62: 852 32.62 - 48.93: 265 48.93 - 65.24: 84 65.24 - 81.55: 20 Dihedral angle restraints: 8060 sinusoidal: 3210 harmonic: 4850 Sorted by residual: dihedral pdb=" CA LYS F 48 " pdb=" C LYS F 48 " pdb=" N ALA F 49 " pdb=" CA ALA F 49 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA LYS E 48 " pdb=" C LYS E 48 " pdb=" N ALA E 49 " pdb=" CA ALA E 49 " ideal model delta harmonic sigma weight residual -180.00 -164.04 -15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LYS C 48 " pdb=" C LYS C 48 " pdb=" N ALA C 49 " pdb=" CA ALA C 49 " ideal model delta harmonic sigma weight residual -180.00 -164.63 -15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1078 0.029 - 0.058: 660 0.058 - 0.087: 158 0.087 - 0.116: 106 0.116 - 0.145: 78 Chirality restraints: 2080 Sorted by residual: chirality pdb=" CA ILE H 167 " pdb=" N ILE H 167 " pdb=" C ILE H 167 " pdb=" CB ILE H 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE E 167 " pdb=" N ILE E 167 " pdb=" C ILE E 167 " pdb=" CB ILE E 167 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 2077 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 122 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C LYS A 122 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS A 122 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 123 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 122 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS J 122 " 0.024 2.00e-02 2.50e+03 pdb=" O LYS J 122 " -0.009 2.00e-02 2.50e+03 pdb=" N LYS J 123 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 42 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 43 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 43 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 43 " 0.018 5.00e-02 4.00e+02 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 6767 2.95 - 3.43: 14141 3.43 - 3.92: 21047 3.92 - 4.41: 25274 4.41 - 4.90: 39778 Nonbonded interactions: 107007 Sorted by model distance: nonbonded pdb=" O MET F 60 " pdb=" O ASP F 62 " model vdw 2.457 3.040 nonbonded pdb=" O MET J 60 " pdb=" O ASP J 62 " model vdw 2.457 3.040 nonbonded pdb=" O MET A 60 " pdb=" O ASP A 62 " model vdw 2.459 3.040 nonbonded pdb=" O MET E 60 " pdb=" O ASP E 62 " model vdw 2.472 3.040 nonbonded pdb=" O MET I 60 " pdb=" O ASP I 62 " model vdw 2.519 3.040 ... (remaining 107002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.050 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: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 : 0.003 0.048 13570 Z= 0.120 Angle : 0.567 5.667 18370 Z= 0.299 Chirality : 0.047 0.145 2080 Planarity : 0.004 0.040 2350 Dihedral : 16.954 81.546 4920 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.96 % Allowed : 24.79 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1650 helix: 2.33 (0.22), residues: 520 sheet: -1.67 (0.28), residues: 320 loop : -1.14 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 180 TYR 0.006 0.001 TYR E 73 PHE 0.013 0.001 PHE G 71 TRP 0.002 0.001 TRP H 116 HIS 0.005 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13570) covalent geometry : angle 0.56704 / 0.30 (18370) hydrogen bonds : bond 0.13174 / 9.06 ( 480) hydrogen bonds : angle 5.01795 / 3.38 ( 1380) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.530 Fit side-chains REVERT: A 131 ILE cc_start: 0.8830 (mm) cc_final: 0.8588 (mt) REVERT: B 131 ILE cc_start: 0.8921 (mm) cc_final: 0.8656 (mt) REVERT: B 190 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8980 (tp-100) REVERT: C 79 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8912 (t80) REVERT: C 131 ILE cc_start: 0.9061 (mm) cc_final: 0.8833 (mt) REVERT: D 131 ILE cc_start: 0.8864 (mm) cc_final: 0.8646 (mt) REVERT: D 190 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8979 (tm-30) REVERT: E 131 ILE cc_start: 0.8828 (mm) cc_final: 0.8604 (mt) REVERT: F 131 ILE cc_start: 0.8758 (mm) cc_final: 0.8531 (mt) REVERT: G 131 ILE cc_start: 0.8866 (mm) cc_final: 0.8650 (mt) REVERT: G 190 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8986 (tm-30) REVERT: H 79 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8957 (t80) REVERT: H 131 ILE cc_start: 0.9043 (mm) cc_final: 0.8814 (mt) REVERT: I 131 ILE cc_start: 0.8901 (mm) cc_final: 0.8635 (mt) REVERT: I 190 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8987 (tp-100) REVERT: J 131 ILE cc_start: 0.8887 (mm) cc_final: 0.8649 (mt) outliers start: 14 outliers final: 9 residues processed: 136 average time/residue: 0.0997 time to fit residues: 20.9039 Evaluate side-chains 116 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 79 PHE Chi-restraints excluded: chain H residue 156 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN C 190 GLN H 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.041568 restraints weight = 39285.465| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 4.53 r_work: 0.2441 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13570 Z= 0.111 Angle : 0.501 4.314 18370 Z= 0.268 Chirality : 0.047 0.170 2080 Planarity : 0.003 0.023 2350 Dihedral : 5.655 59.290 1801 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.36 % Allowed : 22.60 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.22), residues: 1650 helix: 2.58 (0.22), residues: 530 sheet: -1.20 (0.30), residues: 320 loop : -0.65 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 39 TYR 0.013 0.002 TYR C 194 PHE 0.006 0.001 PHE E 71 TRP 0.002 0.001 TRP I 116 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13570) covalent geometry : angle 0.50113 / 0.27 (18370) hydrogen bonds : bond 0.02899 / 1.91 ( 480) hydrogen bonds : angle 3.57185 / 2.45 ( 1380) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.510 Fit side-chains REVERT: B 131 ILE cc_start: 0.8643 (mm) cc_final: 0.8363 (mt) REVERT: B 154 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8692 (pp) REVERT: B 190 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8923 (tp-100) REVERT: E 131 ILE cc_start: 0.8662 (mm) cc_final: 0.8404 (mt) REVERT: F 131 ILE cc_start: 0.8650 (mm) cc_final: 0.8393 (mt) REVERT: I 131 ILE cc_start: 0.8651 (mm) cc_final: 0.8368 (mt) REVERT: I 190 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8926 (tp-100) outliers start: 49 outliers final: 24 residues processed: 161 average time/residue: 0.1057 time to fit residues: 25.2617 Evaluate side-chains 122 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 79 PHE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 63 TYR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [109, 141, 119, 26, 87, 11, 73, 158, 53, 48, 57] chunk 109 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.039504 restraints weight = 40120.931| |-----------------------------------------------------------------------------| r_work (start): 0.2559 rms_B_bonded: 4.52 r_work: 0.2391 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13570 Z= 0.185 Angle : 0.514 5.268 18370 Z= 0.273 Chirality : 0.047 0.156 2080 Planarity : 0.003 0.025 2350 Dihedral : 4.240 59.566 1784 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.29 % Allowed : 22.26 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1650 helix: 2.62 (0.22), residues: 530 sheet: -0.95 (0.30), residues: 320 loop : -0.57 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 39 TYR 0.006 0.001 TYR J 145 PHE 0.009 0.001 PHE D 72 TRP 0.003 0.001 TRP E 116 HIS 0.002 0.001 HIS J 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (13570) covalent geometry : angle 0.51393 / 0.27 (18370) hydrogen bonds : bond 0.03405 / 2.25 ( 480) hydrogen bonds : angle 3.75836 / 2.59 ( 1380) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 131 ILE cc_start: 0.8654 (mm) cc_final: 0.8377 (mt) REVERT: B 190 GLN cc_start: 0.9279 (tm-30) cc_final: 0.9001 (tp-100) REVERT: I 131 ILE cc_start: 0.8639 (mm) cc_final: 0.8352 (mt) REVERT: I 190 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8980 (tp-100) outliers start: 48 outliers final: 32 residues processed: 149 average time/residue: 0.1017 time to fit residues: 23.0900 Evaluate side-chains 122 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 130 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [57, 106, 148, 157, 16, 30, 41, 146, 73, 11, 88] chunk 57 optimal weight: 0.0370 chunk 106 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 73 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.040479 restraints weight = 39739.931| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 4.51 r_work: 0.2421 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13570 Z= 0.122 Angle : 0.493 8.314 18370 Z= 0.256 Chirality : 0.046 0.147 2080 Planarity : 0.003 0.026 2350 Dihedral : 3.534 15.493 1780 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.15 % Allowed : 21.71 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.22), residues: 1650 helix: 2.57 (0.22), residues: 530 sheet: -0.91 (0.30), residues: 320 loop : -0.49 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 180 TYR 0.018 0.001 TYR C 194 PHE 0.006 0.001 PHE D 72 TRP 0.002 0.001 TRP E 116 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (13570) covalent geometry : angle 0.49330 / 0.26 (18370) hydrogen bonds : bond 0.02791 / 1.84 ( 480) hydrogen bonds : angle 3.53433 / 2.44 ( 1380) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 131 ILE cc_start: 0.8535 (mm) cc_final: 0.8247 (mt) REVERT: B 190 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8964 (tp-100) REVERT: D 40 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8830 (mt-10) REVERT: G 194 TYR cc_start: 0.9025 (t80) cc_final: 0.8796 (t80) REVERT: I 131 ILE cc_start: 0.8557 (mm) cc_final: 0.8265 (mt) REVERT: I 190 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8960 (tp-100) outliers start: 46 outliers final: 25 residues processed: 144 average time/residue: 0.0976 time to fit residues: 21.3417 Evaluate side-chains 120 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [71, 24, 70, 59, 137, 150, 153, 104, 84, 27, 154] chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN C 190 GLN H 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.039809 restraints weight = 39938.024| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 4.50 r_work: 0.2399 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13570 Z= 0.159 Angle : 0.505 6.801 18370 Z= 0.263 Chirality : 0.046 0.148 2080 Planarity : 0.003 0.026 2350 Dihedral : 3.583 14.752 1780 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.11 % Allowed : 20.27 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1650 helix: 2.59 (0.22), residues: 530 sheet: -0.80 (0.31), residues: 320 loop : -0.38 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 39 TYR 0.011 0.001 TYR H 194 PHE 0.008 0.001 PHE D 72 TRP 0.002 0.001 TRP E 116 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (13570) covalent geometry : angle 0.50528 / 0.26 (18370) hydrogen bonds : bond 0.03085 / 2.04 ( 480) hydrogen bonds : angle 3.62351 / 2.50 ( 1380) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 131 ILE cc_start: 0.8601 (mm) cc_final: 0.8323 (mt) REVERT: B 190 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8982 (tp-100) REVERT: D 40 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8850 (mt-10) REVERT: I 131 ILE cc_start: 0.8617 (mm) cc_final: 0.8335 (mt) REVERT: I 190 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8983 (tp-100) outliers start: 60 outliers final: 38 residues processed: 154 average time/residue: 0.0936 time to fit residues: 21.6839 Evaluate side-chains 131 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 130 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [3, 25, 150, 147, 131, 47, 139, 27, 112, 144, 16] chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 190 GLN E 190 GLN F 190 GLN H 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.038488 restraints weight = 40271.614| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 4.49 r_work: 0.2364 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13570 Z= 0.234 Angle : 0.549 5.389 18370 Z= 0.288 Chirality : 0.047 0.151 2080 Planarity : 0.003 0.029 2350 Dihedral : 3.827 16.212 1780 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.97 % Allowed : 20.96 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1650 helix: 2.53 (0.22), residues: 530 sheet: -0.82 (0.32), residues: 320 loop : -0.42 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 39 TYR 0.025 0.001 TYR G 194 PHE 0.011 0.001 PHE D 72 TRP 0.003 0.001 TRP E 116 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (13570) covalent geometry : angle 0.54947 / 0.29 (18370) hydrogen bonds : bond 0.03561 / 2.35 ( 480) hydrogen bonds : angle 3.81994 / 2.64 ( 1380) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 131 ILE cc_start: 0.8677 (mm) cc_final: 0.8411 (mt) REVERT: B 190 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8989 (tp-100) REVERT: D 40 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8876 (mm-30) REVERT: I 131 ILE cc_start: 0.8693 (mm) cc_final: 0.8427 (mt) REVERT: I 190 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8974 (tp-100) outliers start: 58 outliers final: 42 residues processed: 149 average time/residue: 0.1033 time to fit residues: 23.3986 Evaluate side-chains 135 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [116, 148, 72, 152, 111, 19, 56, 142, 15, 61, 36] chunk 116 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 190 GLN F 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.041092 restraints weight = 39788.698| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 4.49 r_work: 0.2420 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13570 Z= 0.115 Angle : 0.486 5.665 18370 Z= 0.255 Chirality : 0.045 0.145 2080 Planarity : 0.003 0.031 2350 Dihedral : 3.515 15.228 1780 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.77 % Allowed : 21.23 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1650 helix: 2.61 (0.22), residues: 530 sheet: -0.79 (0.32), residues: 320 loop : -0.37 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 39 TYR 0.011 0.001 TYR F 194 PHE 0.006 0.001 PHE I 72 TRP 0.003 0.001 TRP G 116 HIS 0.002 0.000 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13570) covalent geometry : angle 0.48572 / 0.26 (18370) hydrogen bonds : bond 0.02638 / 1.74 ( 480) hydrogen bonds : angle 3.46693 / 2.41 ( 1380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 190 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8940 (tp-100) REVERT: C 194 TYR cc_start: 0.9148 (t80) cc_final: 0.8936 (t80) REVERT: D 40 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8854 (mm-30) REVERT: H 91 SER cc_start: 0.9206 (m) cc_final: 0.8697 (p) REVERT: H 194 TYR cc_start: 0.9116 (t80) cc_final: 0.8891 (t80) REVERT: I 154 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8674 (pp) REVERT: I 190 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8943 (tp-100) outliers start: 55 outliers final: 36 residues processed: 153 average time/residue: 0.1035 time to fit residues: 23.7068 Evaluate side-chains 128 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 190 GLN Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 135, 37, 67, 104, 19, 52, 51, 10, 108, 109] chunk 98 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 0.0070 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN C 190 GLN E 190 GLN F 190 GLN H 190 GLN J 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.041125 restraints weight = 39552.837| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 4.49 r_work: 0.2424 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13570 Z= 0.117 Angle : 0.485 5.300 18370 Z= 0.255 Chirality : 0.045 0.142 2080 Planarity : 0.003 0.030 2350 Dihedral : 3.464 14.906 1780 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.49 % Allowed : 21.37 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1650 helix: 2.68 (0.22), residues: 530 sheet: -0.77 (0.32), residues: 320 loop : -0.30 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 39 TYR 0.026 0.001 TYR G 194 PHE 0.006 0.001 PHE G 72 TRP 0.003 0.001 TRP G 116 HIS 0.001 0.000 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13570) covalent geometry : angle 0.48503 / 0.25 (18370) hydrogen bonds : bond 0.02717 / 1.80 ( 480) hydrogen bonds : angle 3.46830 / 2.41 ( 1380) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 190 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8925 (tp-100) REVERT: C 91 SER cc_start: 0.9228 (m) cc_final: 0.8706 (p) REVERT: C 194 TYR cc_start: 0.9176 (t80) cc_final: 0.8942 (t80) REVERT: D 40 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8865 (mm-30) REVERT: G 103 ILE cc_start: 0.8834 (mt) cc_final: 0.8608 (mm) REVERT: H 91 SER cc_start: 0.9198 (m) cc_final: 0.8679 (p) REVERT: H 194 TYR cc_start: 0.9146 (t80) cc_final: 0.8909 (t80) REVERT: I 154 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8666 (pp) REVERT: I 190 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8931 (tp-100) outliers start: 51 outliers final: 36 residues processed: 144 average time/residue: 0.1021 time to fit residues: 21.8855 Evaluate side-chains 132 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 63 TYR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [132, 79, 33, 87, 10, 139, 127, 11, 107, 141, 42] chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.041398 restraints weight = 39874.110| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 4.51 r_work: 0.2436 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13570 Z= 0.112 Angle : 0.482 5.614 18370 Z= 0.253 Chirality : 0.045 0.141 2080 Planarity : 0.003 0.030 2350 Dihedral : 3.383 14.911 1780 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.22 % Allowed : 21.10 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1650 helix: 2.69 (0.22), residues: 530 sheet: -0.77 (0.32), residues: 320 loop : -0.26 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 39 TYR 0.016 0.001 TYR E 194 PHE 0.005 0.001 PHE B 72 TRP 0.003 0.001 TRP C 116 HIS 0.001 0.000 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (13570) covalent geometry : angle 0.48203 / 0.25 (18370) hydrogen bonds : bond 0.02560 / 1.69 ( 480) hydrogen bonds : angle 3.40873 / 2.38 ( 1380) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 190 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8931 (tp-100) REVERT: C 91 SER cc_start: 0.9252 (m) cc_final: 0.8725 (p) REVERT: C 194 TYR cc_start: 0.9110 (t80) cc_final: 0.8875 (t80) REVERT: D 40 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8869 (mm-30) REVERT: D 103 ILE cc_start: 0.8793 (mt) cc_final: 0.8571 (mm) REVERT: G 103 ILE cc_start: 0.8837 (mt) cc_final: 0.8620 (mm) REVERT: H 91 SER cc_start: 0.9260 (m) cc_final: 0.8736 (p) REVERT: H 194 TYR cc_start: 0.9106 (t80) cc_final: 0.8865 (t80) REVERT: I 154 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8684 (pp) REVERT: I 190 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8934 (tp-100) outliers start: 47 outliers final: 35 residues processed: 141 average time/residue: 0.1060 time to fit residues: 22.6142 Evaluate side-chains 125 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 154 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [48, 79, 47, 49, 133, 149, 112, 147, 152, 38, 139] chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN C 190 GLN H 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.039263 restraints weight = 40214.359| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 4.50 r_work: 0.2387 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13570 Z= 0.184 Angle : 0.521 4.916 18370 Z= 0.275 Chirality : 0.046 0.139 2080 Planarity : 0.003 0.030 2350 Dihedral : 3.643 15.487 1780 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.95 % Allowed : 21.44 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.22), residues: 1650 helix: 2.68 (0.22), residues: 530 sheet: -0.78 (0.33), residues: 320 loop : -0.26 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 39 TYR 0.025 0.001 TYR G 194 PHE 0.009 0.001 PHE G 72 TRP 0.002 0.001 TRP D 116 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (13570) covalent geometry : angle 0.52114 / 0.28 (18370) hydrogen bonds : bond 0.03205 / 2.11 ( 480) hydrogen bonds : angle 3.66840 / 2.55 ( 1380) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 190 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9004 (tp-100) REVERT: C 91 SER cc_start: 0.9266 (m) cc_final: 0.8733 (p) REVERT: C 194 TYR cc_start: 0.9100 (t80) cc_final: 0.8880 (t80) REVERT: D 129 MET cc_start: 0.9281 (tpt) cc_final: 0.9064 (tpt) REVERT: H 91 SER cc_start: 0.9269 (m) cc_final: 0.8737 (p) REVERT: I 190 GLN cc_start: 0.9324 (tm-30) cc_final: 0.9005 (tp-100) outliers start: 43 outliers final: 37 residues processed: 130 average time/residue: 0.0882 time to fit residues: 18.3493 Evaluate side-chains 121 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 84 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 130 LYS Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [129, 39, 57, 112, 22, 5, 15, 64, 142, 1, 80] chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.057229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.038875 restraints weight = 40375.685| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 4.48 r_work: 0.2377 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13570 Z= 0.201 Angle : 0.538 7.007 18370 Z= 0.283 Chirality : 0.047 0.145 2080 Planarity : 0.003 0.030 2350 Dihedral : 3.739 15.807 1780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.81 % Allowed : 21.85 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1650 helix: 2.60 (0.22), residues: 530 sheet: -0.86 (0.32), residues: 320 loop : -0.32 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 39 TYR 0.018 0.001 TYR H 194 PHE 0.009 0.001 PHE D 72 TRP 0.003 0.001 TRP G 116 HIS 0.002 0.001 HIS I 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (13570) covalent geometry : angle 0.53774 / 0.28 (18370) hydrogen bonds : bond 0.03299 / 2.18 ( 480) hydrogen bonds : angle 3.71620 / 2.59 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.57 seconds wall clock time: 42 minutes 37.77 seconds (2557.77 seconds total)