Starting phenix.real_space_refine on Wed Feb 4 17:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3l_47487/02_2026/9e3l_47487.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3l_47487/02_2026/9e3l_47487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3l_47487/02_2026/9e3l_47487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3l_47487/02_2026/9e3l_47487.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3l_47487/02_2026/9e3l_47487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3l_47487/02_2026/9e3l_47487.cif" } resolution = 3.4 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= 0.000 sd= 0.011 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 72 5.16 5 C 7543 2.51 5 N 2039 2.21 5 O 2277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11931 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1769 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 882 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1521 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 96} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 96} Chain: "F" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 989 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "H" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 865 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "J" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 799 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "K" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 948 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 814 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 2.25, per 1000 atoms: 0.19 Number of scatterers: 11931 At special positions: 0 Unit cell: (87.36, 139.44, 147, 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 72 16.00 O 2277 8.00 N 2039 7.00 C 7543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 199 " distance=2.04 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 199 " distance=2.03 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 51 " distance=2.06 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 41 " distance=2.05 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 473.6 milliseconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 13.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 removed outlier: 3.872A pdb=" N VAL A 18 " --> pdb=" O PRO A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 57 through 77 Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.153A pdb=" N TYR A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 4.948A pdb=" N LYS B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.634A pdb=" N LEU C 12 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 37 removed outlier: 3.585A pdb=" N LEU C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 145 through 159 removed outlier: 3.661A pdb=" N LEU C 149 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.812A pdb=" N SER C 197 " --> pdb=" O PRO C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'F' and resid 51 through 66 Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.803A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 34 Processing helix chain 'K' and resid 25 through 31 Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.600A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing helix chain 'L' and resid 30 through 34 removed outlier: 3.506A pdb=" N TYR L 34 " --> pdb=" O SER L 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.538A pdb=" N ARG A 143 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG A 92 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 141 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 114 removed outlier: 4.730A pdb=" N LEU B 111 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS B 120 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 119 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS B 134 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 121 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY B 132 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE B 123 " --> pdb=" O VAL B 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 128 through 135 current: chain 'B' and resid 182 through 191 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 182 through 191 current: chain 'D' and resid 78 through 82 removed outlier: 4.874A pdb=" N ARG D 99 " --> pdb=" O PHE D 81 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 99 through 102 current: chain 'F' and resid 25 through 31 Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 92 through 93 current: chain 'C' and resid 119 through 125 removed outlier: 3.636A pdb=" N ILE C 131 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG C 125 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 128 through 135 current: chain 'C' and resid 184 through 191 removed outlier: 10.229A pdb=" N THR C 187 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL D 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 33 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL D 16 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS D 31 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET D 18 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 29 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG D 27 " --> pdb=" O PRO D 20 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 48 through 55 current: chain 'D' and resid 92 through 96 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 96 current: chain 'E' and resid 27 through 36 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 48 through 55 current: chain 'E' and resid 92 through 102 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 102 current: chain 'F' and resid 71 through 75 removed outlier: 4.293A pdb=" N GLU F 88 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLU F 75 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU F 86 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 20 Processing sheet with id=AA9, first strand: chain 'H' and resid 70 through 72 Processing sheet with id=AB1, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AB2, first strand: chain 'I' and resid 45 through 51 removed outlier: 5.436A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'J' and resid 9 through 10 Processing sheet with id=AB5, first strand: chain 'J' and resid 47 through 50 removed outlier: 5.802A pdb=" N THR J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN J 39 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 11 removed outlier: 5.693A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'L' and resid 36 through 40 removed outlier: 6.640A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR L 51 " --> pdb=" O ASN L 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 55 through 56 current: chain 'L' and resid 98 through 101 308 hydrogen bonds defined for protein. 801 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: 1.26 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3855 1.35 - 1.48: 3265 1.48 - 1.61: 4987 1.61 - 1.74: 0 1.74 - 1.88: 108 Bond restraints: 12215 Sorted by residual: bond pdb=" N PRO H 18 " pdb=" CD PRO H 18 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO G 113 " pdb=" CD PRO G 113 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" N PRO H 8 " pdb=" CD PRO H 8 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N PRO H 15 " pdb=" CD PRO H 15 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.42e+01 ... (remaining 12210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 16333 2.67 - 5.35: 201 5.35 - 8.02: 37 8.02 - 10.70: 5 10.70 - 13.37: 19 Bond angle restraints: 16595 Sorted by residual: angle pdb=" CA PRO G 62 " pdb=" N PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 112.00 98.63 13.37 1.40e+00 5.10e-01 9.12e+01 angle pdb=" CA PRO H 18 " pdb=" N PRO H 18 " pdb=" CD PRO H 18 " ideal model delta sigma weight residual 112.00 98.65 13.35 1.40e+00 5.10e-01 9.10e+01 angle pdb=" CA PRO G 113 " pdb=" N PRO G 113 " pdb=" CD PRO G 113 " ideal model delta sigma weight residual 112.00 98.86 13.14 1.40e+00 5.10e-01 8.81e+01 angle pdb=" CA PRO H 15 " pdb=" N PRO H 15 " pdb=" CD PRO H 15 " ideal model delta sigma weight residual 112.00 98.89 13.11 1.40e+00 5.10e-01 8.77e+01 angle pdb=" CA PRO H 100 " pdb=" N PRO H 100 " pdb=" CD PRO H 100 " ideal model delta sigma weight residual 112.00 98.96 13.04 1.40e+00 5.10e-01 8.67e+01 ... (remaining 16590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6218 17.74 - 35.49: 758 35.49 - 53.23: 215 53.23 - 70.98: 37 70.98 - 88.72: 16 Dihedral angle restraints: 7244 sinusoidal: 2806 harmonic: 4438 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 90 " pdb=" CB CYS L 90 " ideal model delta sinusoidal sigma weight residual -86.00 -23.95 -62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS E 103 " pdb=" SG CYS E 103 " pdb=" SG CYS E 109 " pdb=" CB CYS E 109 " ideal model delta sinusoidal sigma weight residual 93.00 32.35 60.65 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS F 27 " pdb=" SG CYS F 27 " pdb=" SG CYS F 41 " pdb=" CB CYS F 41 " ideal model delta sinusoidal sigma weight residual 93.00 34.23 58.77 1 1.00e+01 1.00e-02 4.62e+01 ... (remaining 7241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1222 0.038 - 0.075: 390 0.075 - 0.113: 150 0.113 - 0.150: 39 0.150 - 0.188: 22 Chirality restraints: 1823 Sorted by residual: chirality pdb=" CA ILE G 124 " pdb=" N ILE G 124 " pdb=" C ILE G 124 " pdb=" CB ILE G 124 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB THR G 65 " pdb=" CA THR G 65 " pdb=" OG1 THR G 65 " pdb=" CG2 THR G 65 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CB THR G 100 " pdb=" CA THR G 100 " pdb=" OG1 THR G 100 " pdb=" CG2 THR G 100 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1820 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 63 " -0.118 5.00e-02 4.00e+02 1.66e-01 4.41e+01 pdb=" N PRO H 64 " 0.287 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 48 " -0.117 5.00e-02 4.00e+02 1.64e-01 4.32e+01 pdb=" N PRO H 49 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO H 49 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO H 49 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 14 " -0.116 5.00e-02 4.00e+02 1.62e-01 4.19e+01 pdb=" N PRO H 15 " 0.279 5.00e-02 4.00e+02 pdb=" CA PRO H 15 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO H 15 " -0.080 5.00e-02 4.00e+02 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.19: 46 1.19 - 2.12: 230 2.12 - 3.05: 8210 3.05 - 3.97: 31226 3.97 - 4.90: 56739 Warning: very small nonbonded interaction distances. Nonbonded interactions: 96451 Sorted by model distance: nonbonded pdb=" NE1 TRP G 37 " pdb=" O PHE G 79 " model vdw 0.268 3.120 nonbonded pdb=" CZ3 TRP G 35 " pdb=" C ARG G 98 " model vdw 0.439 2.856 nonbonded pdb=" OG SER H 25 " pdb=" CD2 PHE H 76 " model vdw 0.563 3.340 nonbonded pdb=" CZ3 TRP G 34 " pdb=" CD2 TYR G 53 " model vdw 0.563 3.640 nonbonded pdb=" CA PHE G 95 " pdb=" CZ3 TRP G 120 " model vdw 0.583 3.770 ... (remaining 96446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 1 through 108) } 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: 19.780 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 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 : 0.015 0.862 12246 Z= 1.408 Angle : 0.888 13.371 16625 Z= 0.500 Chirality : 0.048 0.188 1823 Planarity : 0.011 0.166 2132 Dihedral : 16.751 88.724 4395 Min Nonbonded Distance : 0.268 Molprobity Statistics. All-atom Clashscore : 50.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 0.39 % Allowed : 25.74 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -1.72 (0.21), residues: 1522 helix: -1.15 (0.34), residues: 184 sheet: 0.05 (0.25), residues: 417 loop : -1.80 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 172 TYR 0.047 0.002 TYR B 146 PHE 0.019 0.002 PHE F 26 TRP 0.021 0.001 TRP L 59 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00454 (12215) covalent geometry : angle 0.88547 (16595) SS BOND : bond 0.00862 ( 15) SS BOND : angle 1.92997 ( 30) hydrogen bonds : bond 0.16074 ( 308) hydrogen bonds : angle 7.21183 ( 801) Misc. bond : bond 0.38457 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8659 (mp) cc_final: 0.8439 (mt) REVERT: D 11 MET cc_start: 0.6479 (ppp) cc_final: 0.6238 (ppp) REVERT: E 75 GLN cc_start: 0.6870 (tm-30) cc_final: 0.6582 (tm-30) REVERT: K 31 ASN cc_start: 0.7500 (m-40) cc_final: 0.7170 (m-40) outliers start: 5 outliers final: 3 residues processed: 203 average time/residue: 0.1057 time to fit residues: 30.3366 Evaluate side-chains 199 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain J residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.0970 chunk 149 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN I 6 GLN I 39 GLN J 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.191614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.170818 restraints weight = 18720.420| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.56 r_work: 0.4102 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 1.816 12246 Z= 0.614 Angle : 0.919 25.257 16625 Z= 0.471 Chirality : 0.051 0.490 1823 Planarity : 0.008 0.081 2132 Dihedral : 6.446 73.386 1729 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.62 % Favored : 92.18 % Rotamer: Outliers : 4.68 % Allowed : 23.63 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.67 (0.21), residues: 1522 helix: -0.44 (0.36), residues: 186 sheet: -0.19 (0.25), residues: 435 loop : -1.80 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 98 TYR 0.033 0.003 TYR G 53 PHE 0.056 0.003 PHE G 116 TRP 0.060 0.005 TRP G 34 HIS 0.006 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.01849 (12215) covalent geometry : angle 0.91659 (16595) SS BOND : bond 0.00750 ( 15) SS BOND : angle 1.80615 ( 30) hydrogen bonds : bond 0.05119 ( 308) hydrogen bonds : angle 6.36396 ( 801) Misc. bond : bond 0.00713 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4208 (pt) REVERT: C 83 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7129 (ttp80) REVERT: D 43 SER cc_start: 0.6300 (p) cc_final: 0.5551 (t) REVERT: E 75 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6411 (tm-30) REVERT: E 108 ASP cc_start: 0.7199 (m-30) cc_final: 0.6980 (m-30) REVERT: F 37 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6632 (tt) REVERT: H 98 GLN cc_start: 0.5863 (tt0) cc_final: 0.4309 (mp10) REVERT: I 38 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6922 (ptp-170) REVERT: K 31 ASN cc_start: 0.7412 (m-40) cc_final: 0.7113 (m-40) outliers start: 60 outliers final: 35 residues processed: 229 average time/residue: 0.1021 time to fit residues: 33.2098 Evaluate side-chains 224 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 121 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.191396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.170668 restraints weight = 18786.745| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.56 r_work: 0.4106 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12246 Z= 0.210 Angle : 0.772 14.730 16625 Z= 0.401 Chirality : 0.047 0.291 1823 Planarity : 0.006 0.063 2132 Dihedral : 6.229 78.606 1725 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.72 % Rotamer: Outliers : 5.69 % Allowed : 23.17 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.63 (0.21), residues: 1522 helix: -0.17 (0.38), residues: 180 sheet: -0.19 (0.25), residues: 430 loop : -1.79 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 98 TYR 0.023 0.002 TYR C 157 PHE 0.031 0.002 PHE G 95 TRP 0.046 0.004 TRP G 34 HIS 0.005 0.001 HIS L 33 Details of bonding type rmsd covalent geometry : bond 0.00489 (12215) covalent geometry : angle 0.76933 (16595) SS BOND : bond 0.00758 ( 15) SS BOND : angle 1.81076 ( 30) hydrogen bonds : bond 0.04473 ( 308) hydrogen bonds : angle 6.24530 ( 801) Misc. bond : bond 0.00495 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 201 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.4942 (OUTLIER) cc_final: 0.4279 (pt) REVERT: B 148 ARG cc_start: 0.5942 (OUTLIER) cc_final: 0.3948 (mtt180) REVERT: C 83 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7158 (ttp80) REVERT: C 126 ASP cc_start: 0.7677 (t0) cc_final: 0.7335 (t0) REVERT: C 153 LEU cc_start: 0.8070 (tp) cc_final: 0.7763 (tt) REVERT: D 11 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6161 (ppp) REVERT: D 67 MET cc_start: 0.7992 (ttt) cc_final: 0.7507 (ttt) REVERT: E 75 GLN cc_start: 0.6567 (tm-30) cc_final: 0.5687 (tt0) REVERT: E 108 ASP cc_start: 0.7328 (m-30) cc_final: 0.6951 (m-30) REVERT: F 37 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6701 (tt) REVERT: F 56 MET cc_start: 0.6131 (tpt) cc_final: 0.5899 (tpt) REVERT: H 98 GLN cc_start: 0.5889 (tt0) cc_final: 0.4392 (mp10) REVERT: I 10 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.5075 (tp30) REVERT: I 35 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7075 (m90) REVERT: I 38 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7061 (ptp-170) REVERT: I 64 PHE cc_start: 0.7119 (m-80) cc_final: 0.6446 (m-80) REVERT: J 37 TRP cc_start: 0.7255 (m100) cc_final: 0.6929 (m100) REVERT: K 31 ASN cc_start: 0.7367 (m-40) cc_final: 0.7020 (m-40) REVERT: L 63 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6076 (ptt-90) REVERT: L 98 ARG cc_start: 0.5383 (OUTLIER) cc_final: 0.5003 (mmp-170) outliers start: 73 outliers final: 50 residues processed: 257 average time/residue: 0.1087 time to fit residues: 39.0674 Evaluate side-chains 252 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 114 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 116 optimal weight: 0.2980 chunk 118 optimal weight: 0.0670 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.192043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.171082 restraints weight = 18868.735| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.64 r_work: 0.4109 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12246 Z= 0.180 Angle : 0.732 12.723 16625 Z= 0.381 Chirality : 0.046 0.298 1823 Planarity : 0.006 0.055 2132 Dihedral : 6.096 83.962 1725 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.34 % Favored : 91.59 % Rotamer: Outliers : 6.08 % Allowed : 24.26 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.58 (0.21), residues: 1522 helix: -0.08 (0.38), residues: 185 sheet: -0.17 (0.25), residues: 429 loop : -1.77 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 172 TYR 0.026 0.002 TYR C 173 PHE 0.017 0.002 PHE G 117 TRP 0.049 0.004 TRP G 34 HIS 0.006 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00428 (12215) covalent geometry : angle 0.72828 (16595) SS BOND : bond 0.00871 ( 15) SS BOND : angle 1.80957 ( 30) hydrogen bonds : bond 0.04185 ( 308) hydrogen bonds : angle 6.15434 ( 801) Misc. bond : bond 0.00524 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ILE cc_start: 0.4919 (OUTLIER) cc_final: 0.4256 (pt) REVERT: A 143 ARG cc_start: 0.6678 (mmm160) cc_final: 0.6475 (mmm160) REVERT: A 162 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7323 (m) REVERT: C 83 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7178 (ttp80) REVERT: C 126 ASP cc_start: 0.7735 (t0) cc_final: 0.7372 (t0) REVERT: C 153 LEU cc_start: 0.7988 (tp) cc_final: 0.7667 (tt) REVERT: D 11 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6185 (ppp) REVERT: D 67 MET cc_start: 0.7968 (ttt) cc_final: 0.7511 (ttt) REVERT: E 75 GLN cc_start: 0.6467 (tm-30) cc_final: 0.5748 (tt0) REVERT: F 18 LYS cc_start: 0.6860 (tppt) cc_final: 0.6623 (tppt) REVERT: F 37 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6676 (tt) REVERT: H 21 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6745 (mt) REVERT: I 10 GLU cc_start: 0.5564 (OUTLIER) cc_final: 0.5190 (tp30) REVERT: I 35 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7157 (m90) REVERT: I 38 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6872 (ptp-170) REVERT: K 31 ASN cc_start: 0.7315 (m-40) cc_final: 0.6943 (m-40) REVERT: K 64 PHE cc_start: 0.8270 (m-80) cc_final: 0.8022 (m-80) REVERT: L 98 ARG cc_start: 0.5512 (OUTLIER) cc_final: 0.5009 (mmp-170) outliers start: 78 outliers final: 46 residues processed: 257 average time/residue: 0.1204 time to fit residues: 42.7143 Evaluate side-chains 245 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 142 optimal weight: 0.0980 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.189658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.169391 restraints weight = 18716.235| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.52 r_work: 0.4088 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12246 Z= 0.227 Angle : 0.772 14.115 16625 Z= 0.403 Chirality : 0.048 0.237 1823 Planarity : 0.006 0.053 2132 Dihedral : 6.293 87.629 1725 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 8.03 % Allowed : 23.17 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.68 (0.21), residues: 1522 helix: -0.15 (0.38), residues: 180 sheet: -0.27 (0.25), residues: 424 loop : -1.81 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 172 TYR 0.026 0.002 TYR C 146 PHE 0.020 0.002 PHE G 117 TRP 0.043 0.004 TRP J 37 HIS 0.006 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00533 (12215) covalent geometry : angle 0.76849 (16595) SS BOND : bond 0.01027 ( 15) SS BOND : angle 1.95415 ( 30) hydrogen bonds : bond 0.04670 ( 308) hydrogen bonds : angle 6.28645 ( 801) Misc. bond : bond 0.00407 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 197 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7623 (tmm-80) REVERT: A 141 ILE cc_start: 0.4925 (OUTLIER) cc_final: 0.4297 (pt) REVERT: A 159 THR cc_start: 0.7398 (OUTLIER) cc_final: 0.7127 (m) REVERT: A 162 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7308 (m) REVERT: B 172 GLN cc_start: 0.5641 (OUTLIER) cc_final: 0.5411 (tt0) REVERT: C 83 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7237 (ttp80) REVERT: C 126 ASP cc_start: 0.7730 (t0) cc_final: 0.7415 (t0) REVERT: C 153 LEU cc_start: 0.8007 (tp) cc_final: 0.7672 (tt) REVERT: C 157 TYR cc_start: 0.6189 (t80) cc_final: 0.4828 (t80) REVERT: D 11 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6154 (ppp) REVERT: D 67 MET cc_start: 0.7976 (ttt) cc_final: 0.7705 (ttt) REVERT: E 75 GLN cc_start: 0.6280 (tt0) cc_final: 0.5597 (tt0) REVERT: F 2 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8114 (pp) REVERT: F 37 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6727 (tt) REVERT: H 21 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7085 (mt) REVERT: I 10 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.5147 (tp30) REVERT: I 35 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7075 (m90) REVERT: I 38 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6900 (ptp-170) REVERT: K 31 ASN cc_start: 0.7454 (m-40) cc_final: 0.7148 (m-40) REVERT: K 64 PHE cc_start: 0.8257 (m-80) cc_final: 0.7995 (m-80) REVERT: K 79 VAL cc_start: 0.7429 (p) cc_final: 0.7023 (t) REVERT: L 63 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6135 (ptt-90) REVERT: L 98 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.5061 (mmp-170) outliers start: 103 outliers final: 61 residues processed: 278 average time/residue: 0.1145 time to fit residues: 44.3435 Evaluate side-chains 267 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 67 ARG Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 0.0870 chunk 140 optimal weight: 0.0070 chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.190842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.170067 restraints weight = 18868.305| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.60 r_work: 0.4128 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12246 Z= 0.156 Angle : 0.708 13.278 16625 Z= 0.368 Chirality : 0.046 0.217 1823 Planarity : 0.005 0.054 2132 Dihedral : 5.921 80.174 1725 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 6.16 % Allowed : 25.66 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.51 (0.21), residues: 1522 helix: 0.05 (0.38), residues: 186 sheet: -0.19 (0.25), residues: 423 loop : -1.70 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 148 TYR 0.023 0.002 TYR C 173 PHE 0.019 0.002 PHE G 95 TRP 0.060 0.003 TRP J 37 HIS 0.008 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00372 (12215) covalent geometry : angle 0.70506 (16595) SS BOND : bond 0.00721 ( 15) SS BOND : angle 1.76483 ( 30) hydrogen bonds : bond 0.03965 ( 308) hydrogen bonds : angle 6.04350 ( 801) Misc. bond : bond 0.00361 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 194 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7695 (tmm-80) REVERT: A 141 ILE cc_start: 0.4906 (OUTLIER) cc_final: 0.4296 (pt) REVERT: A 159 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.7035 (m) REVERT: B 151 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7395 (mtmt) REVERT: C 83 ARG cc_start: 0.7625 (ttp80) cc_final: 0.7189 (ttp80) REVERT: C 126 ASP cc_start: 0.7810 (t0) cc_final: 0.7473 (t0) REVERT: C 153 LEU cc_start: 0.7968 (tp) cc_final: 0.7660 (tt) REVERT: D 11 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.6230 (ppp) REVERT: E 75 GLN cc_start: 0.6160 (tt0) cc_final: 0.5563 (tt0) REVERT: F 2 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8130 (pp) REVERT: F 37 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6580 (tt) REVERT: H 21 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6956 (mt) REVERT: I 10 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.5193 (tp30) REVERT: I 38 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6865 (ptp-170) REVERT: K 31 ASN cc_start: 0.7241 (m-40) cc_final: 0.6886 (m-40) REVERT: K 64 PHE cc_start: 0.8256 (m-80) cc_final: 0.8051 (m-80) REVERT: K 79 VAL cc_start: 0.7414 (p) cc_final: 0.6991 (t) REVERT: L 63 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6023 (ptt-90) REVERT: L 98 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.4864 (mmp-170) outliers start: 79 outliers final: 51 residues processed: 258 average time/residue: 0.1156 time to fit residues: 41.4477 Evaluate side-chains 252 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 111 TYR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 94 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.189415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.168861 restraints weight = 18644.016| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.63 r_work: 0.4086 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12246 Z= 0.229 Angle : 0.771 13.162 16625 Z= 0.402 Chirality : 0.047 0.220 1823 Planarity : 0.006 0.051 2132 Dihedral : 6.099 70.397 1725 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 6.47 % Allowed : 25.74 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.71 (0.21), residues: 1522 helix: -0.15 (0.37), residues: 186 sheet: -0.49 (0.25), residues: 437 loop : -1.74 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 148 TYR 0.028 0.002 TYR C 146 PHE 0.022 0.002 PHE G 117 TRP 0.044 0.004 TRP J 37 HIS 0.007 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00539 (12215) covalent geometry : angle 0.76764 (16595) SS BOND : bond 0.00787 ( 15) SS BOND : angle 1.96415 ( 30) hydrogen bonds : bond 0.04620 ( 308) hydrogen bonds : angle 6.32029 ( 801) Misc. bond : bond 0.00368 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 192 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7722 (tmm-80) REVERT: A 141 ILE cc_start: 0.4961 (OUTLIER) cc_final: 0.4308 (pt) REVERT: A 143 ARG cc_start: 0.6776 (mmm160) cc_final: 0.6405 (mmm160) REVERT: A 159 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.7106 (m) REVERT: B 151 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7452 (mtmt) REVERT: C 126 ASP cc_start: 0.7822 (t0) cc_final: 0.7467 (t0) REVERT: C 153 LEU cc_start: 0.8019 (tp) cc_final: 0.7703 (tt) REVERT: D 11 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.6186 (ppp) REVERT: E 73 MET cc_start: 0.5944 (ptp) cc_final: 0.5657 (ptm) REVERT: F 2 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8194 (pp) REVERT: F 37 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6655 (tt) REVERT: H 21 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7198 (mt) REVERT: I 10 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.4694 (tm-30) REVERT: I 35 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.7319 (m90) REVERT: I 38 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6849 (ptp-170) REVERT: K 31 ASN cc_start: 0.7474 (m-40) cc_final: 0.7166 (m-40) REVERT: K 79 VAL cc_start: 0.7479 (p) cc_final: 0.7065 (t) REVERT: L 63 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6135 (ptt-90) REVERT: L 98 ARG cc_start: 0.5544 (OUTLIER) cc_final: 0.5002 (mmp-170) outliers start: 83 outliers final: 59 residues processed: 260 average time/residue: 0.1090 time to fit residues: 39.5008 Evaluate side-chains 255 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 183 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.8980 chunk 107 optimal weight: 0.0010 chunk 75 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 135 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 129 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.191276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.170735 restraints weight = 18753.334| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.63 r_work: 0.4114 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12246 Z= 0.174 Angle : 0.722 12.909 16625 Z= 0.377 Chirality : 0.046 0.208 1823 Planarity : 0.005 0.055 2132 Dihedral : 5.862 62.752 1725 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 6.79 % Allowed : 25.43 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.66 (0.21), residues: 1522 helix: -0.05 (0.38), residues: 187 sheet: -0.23 (0.26), residues: 395 loop : -1.80 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 148 TYR 0.021 0.002 TYR C 146 PHE 0.020 0.002 PHE F 26 TRP 0.082 0.004 TRP J 37 HIS 0.006 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00413 (12215) covalent geometry : angle 0.71304 (16595) SS BOND : bond 0.00739 ( 15) SS BOND : angle 2.79488 ( 30) hydrogen bonds : bond 0.04190 ( 308) hydrogen bonds : angle 6.23581 ( 801) Misc. bond : bond 0.00357 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 185 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7695 (tmm-80) REVERT: A 141 ILE cc_start: 0.4915 (OUTLIER) cc_final: 0.4308 (pt) REVERT: A 159 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.7074 (m) REVERT: B 151 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7401 (mtmt) REVERT: C 126 ASP cc_start: 0.7824 (t0) cc_final: 0.7476 (t0) REVERT: C 153 LEU cc_start: 0.7945 (tp) cc_final: 0.7637 (tt) REVERT: D 11 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.6195 (ppp) REVERT: E 73 MET cc_start: 0.5843 (ptp) cc_final: 0.5568 (ptm) REVERT: E 75 GLN cc_start: 0.6061 (tt0) cc_final: 0.5428 (tt0) REVERT: F 2 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8218 (pp) REVERT: F 37 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6601 (tt) REVERT: H 21 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7177 (mt) REVERT: I 10 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.4772 (tm-30) REVERT: I 38 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6882 (ptp-170) REVERT: K 31 ASN cc_start: 0.7359 (m-40) cc_final: 0.7035 (m-40) REVERT: K 79 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7087 (t) REVERT: K 81 MET cc_start: 0.1819 (ttp) cc_final: 0.1076 (ttp) REVERT: L 63 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.6018 (ptt-90) REVERT: L 98 ARG cc_start: 0.5584 (OUTLIER) cc_final: 0.5029 (mmp-170) outliers start: 87 outliers final: 60 residues processed: 257 average time/residue: 0.1067 time to fit residues: 38.3323 Evaluate side-chains 255 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 182 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 85 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 9 optimal weight: 0.3980 chunk 125 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 96 GLN B 172 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.190976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.170590 restraints weight = 18686.245| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.62 r_work: 0.4108 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12246 Z= 0.184 Angle : 0.738 14.130 16625 Z= 0.382 Chirality : 0.046 0.202 1823 Planarity : 0.005 0.052 2132 Dihedral : 5.854 59.355 1725 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 6.40 % Allowed : 25.90 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.71 (0.21), residues: 1522 helix: -0.04 (0.38), residues: 186 sheet: -0.45 (0.26), residues: 411 loop : -1.76 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 172 TYR 0.022 0.002 TYR C 146 PHE 0.023 0.002 PHE F 26 TRP 0.099 0.004 TRP J 37 HIS 0.006 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00434 (12215) covalent geometry : angle 0.72705 (16595) SS BOND : bond 0.00851 ( 15) SS BOND : angle 3.02234 ( 30) hydrogen bonds : bond 0.04312 ( 308) hydrogen bonds : angle 6.28367 ( 801) Misc. bond : bond 0.00351 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 183 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7698 (tmm-80) REVERT: A 141 ILE cc_start: 0.4938 (OUTLIER) cc_final: 0.4293 (pt) REVERT: A 159 THR cc_start: 0.7344 (OUTLIER) cc_final: 0.7082 (m) REVERT: B 151 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7405 (mtmt) REVERT: C 35 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6078 (mm) REVERT: C 126 ASP cc_start: 0.7845 (t0) cc_final: 0.7498 (t0) REVERT: C 153 LEU cc_start: 0.7925 (tp) cc_final: 0.7619 (tt) REVERT: D 11 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.6163 (ppp) REVERT: E 73 MET cc_start: 0.5837 (ptp) cc_final: 0.5573 (ptm) REVERT: E 75 GLN cc_start: 0.6113 (tt0) cc_final: 0.5488 (tt0) REVERT: F 2 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8233 (pp) REVERT: F 37 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6629 (tt) REVERT: H 21 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7260 (mt) REVERT: I 10 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.4790 (tm-30) REVERT: I 38 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6855 (ptp-170) REVERT: K 31 ASN cc_start: 0.7378 (m-40) cc_final: 0.7045 (m-40) REVERT: K 79 VAL cc_start: 0.7510 (OUTLIER) cc_final: 0.7114 (t) REVERT: L 63 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6122 (ptt-90) REVERT: L 98 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.4982 (mmp-170) outliers start: 82 outliers final: 62 residues processed: 250 average time/residue: 0.1077 time to fit residues: 37.5711 Evaluate side-chains 258 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 182 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 143 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.190228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.169855 restraints weight = 18868.562| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.64 r_work: 0.4099 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12246 Z= 0.195 Angle : 0.752 15.137 16625 Z= 0.389 Chirality : 0.046 0.200 1823 Planarity : 0.006 0.054 2132 Dihedral : 5.918 57.595 1725 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 6.24 % Allowed : 26.21 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.81 (0.21), residues: 1522 helix: -0.08 (0.38), residues: 186 sheet: -0.65 (0.25), residues: 421 loop : -1.77 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 39 TYR 0.023 0.002 TYR C 146 PHE 0.021 0.002 PHE F 26 TRP 0.073 0.004 TRP J 37 HIS 0.006 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00460 (12215) covalent geometry : angle 0.74212 (16595) SS BOND : bond 0.00840 ( 15) SS BOND : angle 2.89451 ( 30) hydrogen bonds : bond 0.04400 ( 308) hydrogen bonds : angle 6.32744 ( 801) Misc. bond : bond 0.00350 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7704 (tmm-80) REVERT: A 141 ILE cc_start: 0.4930 (OUTLIER) cc_final: 0.4287 (pt) REVERT: A 159 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7111 (m) REVERT: B 151 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7437 (mtmt) REVERT: C 126 ASP cc_start: 0.7826 (t0) cc_final: 0.7480 (t0) REVERT: C 153 LEU cc_start: 0.7940 (tp) cc_final: 0.7630 (tt) REVERT: C 157 TYR cc_start: 0.6112 (t80) cc_final: 0.5216 (t80) REVERT: D 11 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6185 (ppp) REVERT: E 73 MET cc_start: 0.5812 (ptp) cc_final: 0.5549 (ptm) REVERT: E 75 GLN cc_start: 0.6035 (tt0) cc_final: 0.5361 (tt0) REVERT: F 2 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8258 (pp) REVERT: F 37 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6644 (tt) REVERT: H 21 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7350 (mt) REVERT: H 23 CYS cc_start: 0.6313 (m) cc_final: 0.6020 (m) REVERT: I 10 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.4812 (tm-30) REVERT: I 35 HIS cc_start: 0.7669 (OUTLIER) cc_final: 0.7318 (m90) REVERT: I 38 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6849 (ptp-170) REVERT: K 31 ASN cc_start: 0.7376 (m-40) cc_final: 0.7062 (m-40) REVERT: K 79 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7173 (t) REVERT: K 81 MET cc_start: 0.1490 (ttp) cc_final: 0.0848 (ttp) REVERT: L 63 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6058 (ptt-90) REVERT: L 98 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.5006 (mmp-170) outliers start: 80 outliers final: 60 residues processed: 251 average time/residue: 0.1014 time to fit residues: 35.6806 Evaluate side-chains 257 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain D residue 11 MET Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 47 HIS Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 35 TRP Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain I residue 10 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 101 PHE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 63 ARG Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 88 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 15 optimal weight: 0.0050 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 0.0670 chunk 20 optimal weight: 0.0370 chunk 99 optimal weight: 0.0770 overall best weight: 0.1168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.194319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.173974 restraints weight = 18848.083| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.64 r_work: 0.4148 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12246 Z= 0.131 Angle : 0.680 12.514 16625 Z= 0.351 Chirality : 0.044 0.183 1823 Planarity : 0.005 0.054 2132 Dihedral : 5.537 57.447 1725 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.91 % Allowed : 27.46 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.61 (0.21), residues: 1522 helix: 0.16 (0.39), residues: 188 sheet: -0.34 (0.26), residues: 406 loop : -1.74 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 39 TYR 0.019 0.001 TYR C 157 PHE 0.023 0.002 PHE F 26 TRP 0.074 0.003 TRP J 37 HIS 0.005 0.001 HIS G 78 Details of bonding type rmsd covalent geometry : bond 0.00310 (12215) covalent geometry : angle 0.67294 (16595) SS BOND : bond 0.00760 ( 15) SS BOND : angle 2.43107 ( 30) hydrogen bonds : bond 0.03749 ( 308) hydrogen bonds : angle 6.08415 ( 801) Misc. bond : bond 0.00355 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.88 seconds wall clock time: 47 minutes 57.58 seconds (2877.58 seconds total)