Starting phenix.real_space_refine on Wed Feb 4 11:28:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3h_47483/02_2026/9e3h_47483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3h_47483/02_2026/9e3h_47483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3h_47483/02_2026/9e3h_47483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3h_47483/02_2026/9e3h_47483.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3h_47483/02_2026/9e3h_47483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3h_47483/02_2026/9e3h_47483.cif" } resolution = 2.9 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= 0.047 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 68 5.16 5 C 6518 2.51 5 N 1750 2.21 5 O 1975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 10311 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1739 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain breaks: 1 Chain: "C" 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': 3, 'TRANS': 108} Chain: "D" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 830 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 97} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 830 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 97} 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: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1522 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "K" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "L" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 879 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "J" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Time building chain proxies: 2.13, per 1000 atoms: 0.21 Number of scatterers: 10311 At special positions: 0 Unit cell: (76.993, 110.637, 153.986, 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 68 16.00 O 1975 8.00 N 1750 7.00 C 6518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 201 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 51 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 109 " distance=2.02 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 41 " distance=2.04 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 87 " 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=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 489.2 milliseconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 18 sheets defined 15.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 4.596A pdb=" N GLN A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 removed outlier: 3.605A pdb=" N HIS A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 removed outlier: 3.700A pdb=" N GLN A 42 " --> pdb=" O ARG A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.911A pdb=" N THR A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.951A pdb=" N GLY A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.915A pdb=" N GLU A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.843A pdb=" N TYR A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.243A pdb=" N ARG C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 62 through 75 removed outlier: 3.621A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.879A pdb=" N HIS E 47 " --> pdb=" O PRO E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 removed outlier: 3.659A pdb=" N MET E 67 " --> pdb=" O PRO E 63 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'B' and resid 18 through 22 removed outlier: 4.244A pdb=" N GLY B 21 " --> pdb=" O SER B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 37 removed outlier: 3.574A pdb=" N LEU B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 65 through 68 Processing helix chain 'B' and resid 145 through 159 removed outlier: 5.044A pdb=" N LYS B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.700A pdb=" N ARG A 143 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG A 92 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 141 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 92 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 91 through 92 current: chain 'C' and resid 119 through 125 removed outlier: 5.985A pdb=" N LEU C 119 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS C 134 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 121 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY C 132 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N PHE C 123 " --> pdb=" O VAL C 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 128 through 134 current: chain 'C' and resid 183 through 191 removed outlier: 9.916A pdb=" N THR C 187 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL D 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE D 33 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL D 16 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N CYS D 31 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET D 18 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU D 29 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 8.306A 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 102 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 102 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 25 through 31 removed outlier: 3.662A pdb=" N PHE F 26 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 42 " --> pdb=" O PHE F 26 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 38 through 43 current: chain 'F' and resid 84 through 91 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 91 current: chain 'B' and resid 119 through 125 removed outlier: 5.911A pdb=" N ARG B 125 " --> pdb=" O PRO B 129 " (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 183 through 190 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.753A pdb=" N LYS H 5 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 23 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR H 72 " --> pdb=" O THR H 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'H' and resid 37 through 43 removed outlier: 6.714A pdb=" N VAL H 38 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU H 54 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP H 40 " --> pdb=" O LEU H 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 61 through 63 current: chain 'H' and resid 115 through 118 Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.326A pdb=" N LEU K 11 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN K 43 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU K 52 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.731A pdb=" N LYS K 36 " --> pdb=" O SER K 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.404A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 21 through 24 removed outlier: 3.948A pdb=" N ASP L 76 " --> pdb=" O SER L 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AB8, first strand: chain 'J' and resid 20 through 22 removed outlier: 5.743A pdb=" N ARG J 81 " --> pdb=" O ASP J 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 62 through 63 removed outlier: 5.633A pdb=" N TRP J 51 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG J 42 " --> pdb=" O TRP J 51 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA J 53 " --> pdb=" O TRP J 40 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE J 117 " --> pdb=" O HIS J 101 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 690 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: 1.33 Time building geometry restraints manager: 1.09 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: 3329 1.35 - 1.48: 2747 1.48 - 1.60: 4369 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 10549 Sorted by residual: bond pdb=" CB PRO J 65 " pdb=" CG PRO J 65 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.86e+00 bond pdb=" CB PRO A 4 " pdb=" CG PRO A 4 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.97e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.32e-02 5.74e+03 2.38e+00 bond pdb=" CB CYS F 27 " pdb=" SG CYS F 27 " ideal model delta sigma weight residual 1.808 1.858 -0.050 3.30e-02 9.18e+02 2.26e+00 bond pdb=" CG PRO A 4 " pdb=" CD PRO A 4 " ideal model delta sigma weight residual 1.503 1.554 -0.051 3.40e-02 8.65e+02 2.26e+00 ... (remaining 10544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 13874 2.16 - 4.32: 393 4.32 - 6.49: 55 6.49 - 8.65: 8 8.65 - 10.81: 7 Bond angle restraints: 14337 Sorted by residual: angle pdb=" C GLN J 120 " pdb=" N GLY J 121 " pdb=" CA GLY J 121 " ideal model delta sigma weight residual 122.33 117.63 4.70 7.30e-01 1.88e+00 4.15e+01 angle pdb=" CA PRO A 4 " pdb=" N PRO A 4 " pdb=" CD PRO A 4 " ideal model delta sigma weight residual 112.00 103.48 8.52 1.40e+00 5.10e-01 3.70e+01 angle pdb=" CA PRO J 65 " pdb=" N PRO J 65 " pdb=" CD PRO J 65 " ideal model delta sigma weight residual 112.00 103.81 8.19 1.40e+00 5.10e-01 3.42e+01 angle pdb=" N ARG K 67 " pdb=" CA ARG K 67 " pdb=" C ARG K 67 " ideal model delta sigma weight residual 113.18 107.50 5.68 1.33e+00 5.65e-01 1.82e+01 angle pdb=" CA PRO L 50 " pdb=" N PRO L 50 " pdb=" CD PRO L 50 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 ... (remaining 14332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5304 17.99 - 35.97: 763 35.97 - 53.96: 218 53.96 - 71.94: 58 71.94 - 89.93: 21 Dihedral angle restraints: 6364 sinusoidal: 2518 harmonic: 3846 Sorted by residual: dihedral pdb=" CA THR K 100 " pdb=" C THR K 100 " pdb=" N PRO K 101 " pdb=" CA PRO K 101 " ideal model delta harmonic sigma weight residual 180.00 127.81 52.19 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA SER K 7 " pdb=" C SER K 7 " pdb=" N PRO K 8 " pdb=" CA PRO K 8 " ideal model delta harmonic sigma weight residual -180.00 -135.33 -44.67 0 5.00e+00 4.00e-02 7.98e+01 dihedral pdb=" CA THR L 100 " pdb=" C THR L 100 " pdb=" N PRO L 101 " pdb=" CA PRO L 101 " ideal model delta harmonic sigma weight residual 180.00 139.09 40.91 0 5.00e+00 4.00e-02 6.70e+01 ... (remaining 6361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1034 0.036 - 0.072: 379 0.072 - 0.107: 128 0.107 - 0.143: 41 0.143 - 0.179: 14 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CB ILE A 85 " pdb=" CA ILE A 85 " pdb=" CG1 ILE A 85 " pdb=" CG2 ILE A 85 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA PRO A 4 " pdb=" N PRO A 4 " pdb=" C PRO A 4 " pdb=" CB PRO A 4 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CB ILE J 33 " pdb=" CA ILE J 33 " pdb=" CG1 ILE J 33 " pdb=" CG2 ILE J 33 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1593 not shown) Planarity restraints: 1843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " 0.062 5.00e-02 4.00e+02 9.44e-02 1.42e+01 pdb=" N PRO K 8 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 64 " -0.065 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO J 65 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO J 65 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 65 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 3 " 0.055 5.00e-02 4.00e+02 7.82e-02 9.79e+00 pdb=" N PRO A 4 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.043 5.00e-02 4.00e+02 ... (remaining 1840 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 197 2.64 - 3.20: 9111 3.20 - 3.77: 16035 3.77 - 4.33: 22652 4.33 - 4.90: 37525 Nonbonded interactions: 85520 Sorted by model distance: nonbonded pdb=" OE2 GLU D 102 " pdb=" OH TYR B 157 " model vdw 2.074 3.040 nonbonded pdb=" OE1 GLU B 182 " pdb=" OH TYR B 184 " model vdw 2.114 3.040 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 103 " model vdw 2.120 3.040 nonbonded pdb=" O ARG C 110 " pdb=" OH TYR C 176 " model vdw 2.141 3.040 nonbonded pdb=" O ASP A 30 " pdb=" OG SER A 180 " model vdw 2.159 3.040 ... (remaining 85515 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 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 6.020 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.350 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 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 : 0.005 0.110 10565 Z= 0.232 Angle : 0.870 10.808 14369 Z= 0.495 Chirality : 0.046 0.179 1596 Planarity : 0.007 0.094 1843 Dihedral : 19.051 89.929 3864 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.25 % Rotamer: Outliers : 5.31 % Allowed : 32.57 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.92 (0.22), residues: 1304 helix: -0.88 (0.39), residues: 168 sheet: -1.13 (0.25), residues: 403 loop : -1.42 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 79 TYR 0.024 0.002 TYR J 98 PHE 0.033 0.003 PHE C 123 TRP 0.013 0.002 TRP F 52 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00519 (10549) covalent geometry : angle 0.86784 (14337) SS BOND : bond 0.00507 ( 16) SS BOND : angle 1.47189 ( 32) hydrogen bonds : bond 0.16342 ( 265) hydrogen bonds : angle 7.25745 ( 690) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7107 (tt0) cc_final: 0.6712 (tp30) REVERT: A 105 PHE cc_start: 0.6686 (m-10) cc_final: 0.6381 (m-80) REVERT: A 134 ARG cc_start: 0.4536 (ttp-110) cc_final: 0.3676 (mtp85) REVERT: C 96 GLN cc_start: 0.5313 (mp10) cc_final: 0.5021 (mt0) REVERT: C 139 GLU cc_start: 0.5663 (pt0) cc_final: 0.5386 (pm20) REVERT: C 143 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7385 (ptm-80) REVERT: C 155 MET cc_start: 0.6156 (tpt) cc_final: 0.5907 (tpt) REVERT: C 158 MET cc_start: 0.6295 (tpp) cc_final: 0.5940 (mmm) REVERT: D 82 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5730 (mp) REVERT: E 100 MET cc_start: 0.6545 (ptm) cc_final: 0.6011 (pp-130) REVERT: E 101 VAL cc_start: 0.7547 (m) cc_final: 0.7331 (t) REVERT: F 13 GLN cc_start: 0.7028 (pt0) cc_final: 0.6672 (pt0) REVERT: F 14 GLU cc_start: 0.5900 (mt-10) cc_final: 0.5272 (mt-10) REVERT: F 91 ILE cc_start: 0.6567 (mt) cc_final: 0.6202 (tt) REVERT: L 14 SER cc_start: 0.6518 (OUTLIER) cc_final: 0.6274 (p) outliers start: 60 outliers final: 24 residues processed: 323 average time/residue: 0.4784 time to fit residues: 167.2649 Evaluate side-chains 228 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 61 SER Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 32 SER Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 35 HIS C 128 GLN B 12 GLN B 96 GLN B 172 GLN K 34 ASN L 85 GLN L 106 GLN J 80 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.209627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.189998 restraints weight = 11767.628| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 1.77 r_work: 0.4252 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4136 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10565 Z= 0.138 Angle : 0.679 7.649 14369 Z= 0.350 Chirality : 0.044 0.162 1596 Planarity : 0.006 0.083 1843 Dihedral : 7.800 55.834 1517 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Rotamer: Outliers : 6.73 % Allowed : 32.04 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.40 (0.23), residues: 1304 helix: 0.25 (0.41), residues: 158 sheet: -0.87 (0.25), residues: 397 loop : -1.20 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 60 TYR 0.023 0.002 TYR J 98 PHE 0.015 0.002 PHE E 52 TRP 0.008 0.001 TRP B 52 HIS 0.005 0.001 HIS J 101 Details of bonding type rmsd covalent geometry : bond 0.00323 (10549) covalent geometry : angle 0.67603 (14337) SS BOND : bond 0.00528 ( 16) SS BOND : angle 1.55307 ( 32) hydrogen bonds : bond 0.03875 ( 265) hydrogen bonds : angle 5.67287 ( 690) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 213 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6423 (mt-10) REVERT: A 105 PHE cc_start: 0.7192 (m-10) cc_final: 0.6982 (m-80) REVERT: A 113 ASP cc_start: 0.7383 (t0) cc_final: 0.7162 (t70) REVERT: C 193 ASN cc_start: 0.6084 (OUTLIER) cc_final: 0.5648 (m-40) REVERT: D 82 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6102 (mt) REVERT: D 95 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6972 (mt) REVERT: E 45 ASP cc_start: 0.5137 (m-30) cc_final: 0.4894 (m-30) REVERT: F 14 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5815 (mt-10) REVERT: B 89 MET cc_start: 0.6339 (pmm) cc_final: 0.4631 (tmm) REVERT: B 152 MET cc_start: 0.7787 (mmm) cc_final: 0.7555 (mmt) REVERT: K 27 GLN cc_start: 0.6347 (OUTLIER) cc_final: 0.6115 (tm130) REVERT: L 14 SER cc_start: 0.8111 (OUTLIER) cc_final: 0.7536 (p) REVERT: J 86 MET cc_start: 0.6859 (ttp) cc_final: 0.4910 (ptm) outliers start: 76 outliers final: 28 residues processed: 262 average time/residue: 0.4060 time to fit residues: 115.8997 Evaluate side-chains 224 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 55 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN C 128 GLN F 47 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN L 38 ASN L 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.204823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.185169 restraints weight = 11852.278| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.69 r_work: 0.4191 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4077 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10565 Z= 0.181 Angle : 0.708 8.606 14369 Z= 0.363 Chirality : 0.045 0.167 1596 Planarity : 0.006 0.085 1843 Dihedral : 7.295 54.510 1500 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.98 % Favored : 93.87 % Rotamer: Outliers : 7.88 % Allowed : 31.33 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.45 (0.23), residues: 1304 helix: 0.12 (0.40), residues: 163 sheet: -0.87 (0.27), residues: 373 loop : -1.25 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 60 TYR 0.023 0.002 TYR J 98 PHE 0.023 0.002 PHE C 123 TRP 0.010 0.001 TRP J 40 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00427 (10549) covalent geometry : angle 0.70533 (14337) SS BOND : bond 0.00645 ( 16) SS BOND : angle 1.48029 ( 32) hydrogen bonds : bond 0.04094 ( 265) hydrogen bonds : angle 5.55998 ( 690) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 202 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7444 (tt0) cc_final: 0.7098 (tp30) REVERT: A 134 ARG cc_start: 0.4898 (OUTLIER) cc_final: 0.4072 (mtp85) REVERT: C 155 MET cc_start: 0.7190 (tpt) cc_final: 0.6899 (tpt) REVERT: C 193 ASN cc_start: 0.6505 (OUTLIER) cc_final: 0.5837 (m-40) REVERT: D 82 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6236 (mp) REVERT: E 100 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6670 (tmm) REVERT: F 14 GLU cc_start: 0.6332 (mt-10) cc_final: 0.5864 (mt-10) REVERT: H 123 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7447 (mmm) REVERT: K 27 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.6062 (tm130) REVERT: K 35 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7122 (mptm) REVERT: J 87 ILE cc_start: 0.5468 (OUTLIER) cc_final: 0.5237 (pt) outliers start: 89 outliers final: 44 residues processed: 260 average time/residue: 0.4540 time to fit residues: 128.0735 Evaluate side-chains 225 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN C 128 GLN F 47 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN L 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.205610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.185793 restraints weight = 11929.355| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 1.71 r_work: 0.4187 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10565 Z= 0.161 Angle : 0.682 9.198 14369 Z= 0.350 Chirality : 0.044 0.178 1596 Planarity : 0.006 0.086 1843 Dihedral : 7.006 53.140 1496 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 7.96 % Allowed : 32.48 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.38 (0.23), residues: 1304 helix: 0.15 (0.40), residues: 163 sheet: -0.77 (0.28), residues: 371 loop : -1.22 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 102 TYR 0.017 0.002 TYR J 98 PHE 0.016 0.002 PHE E 52 TRP 0.009 0.001 TRP K 56 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00381 (10549) covalent geometry : angle 0.67963 (14337) SS BOND : bond 0.00511 ( 16) SS BOND : angle 1.46224 ( 32) hydrogen bonds : bond 0.03696 ( 265) hydrogen bonds : angle 5.48584 ( 690) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 185 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6536 (mt-10) REVERT: A 75 GLU cc_start: 0.7389 (tt0) cc_final: 0.7073 (tp30) REVERT: A 134 ARG cc_start: 0.4935 (OUTLIER) cc_final: 0.4088 (mtp85) REVERT: C 142 TYR cc_start: 0.7814 (m-80) cc_final: 0.7605 (m-80) REVERT: D 82 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6222 (mp) REVERT: E 88 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7181 (p) REVERT: F 14 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5830 (mt-10) REVERT: H 66 SER cc_start: 0.8479 (m) cc_final: 0.8130 (t) REVERT: H 70 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.5012 (mtm-85) REVERT: H 123 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: K 27 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.6081 (tm130) REVERT: K 35 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.7115 (mptm) REVERT: J 98 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6817 (m-80) outliers start: 90 outliers final: 46 residues processed: 250 average time/residue: 0.4221 time to fit residues: 114.7091 Evaluate side-chains 228 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 35 LYS Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 0.0010 chunk 75 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 69 GLN C 128 GLN K 43 GLN L 106 GLN J 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.204545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184965 restraints weight = 11823.678| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 1.71 r_work: 0.4190 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10565 Z= 0.153 Angle : 0.678 10.928 14369 Z= 0.347 Chirality : 0.044 0.277 1596 Planarity : 0.006 0.089 1843 Dihedral : 6.908 51.386 1496 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 7.35 % Allowed : 32.74 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.32 (0.23), residues: 1304 helix: 0.19 (0.40), residues: 162 sheet: -0.65 (0.28), residues: 361 loop : -1.23 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.016 0.002 TYR J 98 PHE 0.015 0.002 PHE E 52 TRP 0.008 0.001 TRP B 52 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00359 (10549) covalent geometry : angle 0.67551 (14337) SS BOND : bond 0.00560 ( 16) SS BOND : angle 1.35746 ( 32) hydrogen bonds : bond 0.03605 ( 265) hydrogen bonds : angle 5.41652 ( 690) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 179 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7376 (tt0) cc_final: 0.7088 (tp30) REVERT: A 79 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.5684 (ttm-80) REVERT: A 134 ARG cc_start: 0.5016 (OUTLIER) cc_final: 0.4134 (mtp85) REVERT: C 142 TYR cc_start: 0.7861 (m-80) cc_final: 0.7633 (m-80) REVERT: C 193 ASN cc_start: 0.6210 (OUTLIER) cc_final: 0.5540 (m-40) REVERT: D 67 MET cc_start: 0.8165 (ttt) cc_final: 0.7905 (ttt) REVERT: D 82 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6224 (mp) REVERT: F 14 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5845 (mt-10) REVERT: H 70 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.4943 (mtm-85) REVERT: H 123 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: K 27 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.6056 (tm130) REVERT: K 53 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7248 (mp) REVERT: J 98 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6854 (m-80) outliers start: 83 outliers final: 52 residues processed: 236 average time/residue: 0.4736 time to fit residues: 121.1341 Evaluate side-chains 229 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 169 GLN C 128 GLN K 34 ASN J 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.203996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.184522 restraints weight = 11908.720| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 1.71 r_work: 0.4185 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10565 Z= 0.151 Angle : 0.677 10.172 14369 Z= 0.346 Chirality : 0.044 0.221 1596 Planarity : 0.006 0.092 1843 Dihedral : 6.810 51.287 1495 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 8.50 % Allowed : 31.59 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.24 (0.23), residues: 1304 helix: 0.23 (0.40), residues: 162 sheet: -0.59 (0.29), residues: 353 loop : -1.17 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.016 0.002 TYR J 98 PHE 0.015 0.002 PHE E 52 TRP 0.007 0.001 TRP B 52 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00359 (10549) covalent geometry : angle 0.67359 (14337) SS BOND : bond 0.00624 ( 16) SS BOND : angle 1.67134 ( 32) hydrogen bonds : bond 0.03520 ( 265) hydrogen bonds : angle 5.37784 ( 690) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 179 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7365 (tt0) cc_final: 0.7071 (tp30) REVERT: A 79 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5670 (ttm-80) REVERT: A 134 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4141 (mtp85) REVERT: C 142 TYR cc_start: 0.7941 (m-80) cc_final: 0.7611 (m-80) REVERT: C 193 ASN cc_start: 0.6189 (OUTLIER) cc_final: 0.5515 (m-40) REVERT: D 82 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6185 (mp) REVERT: E 88 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (p) REVERT: F 14 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5811 (mt-10) REVERT: H 123 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: K 27 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.6048 (tm130) REVERT: K 53 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7158 (mp) REVERT: K 67 ARG cc_start: 0.6556 (ptp90) cc_final: 0.6285 (ptp90) REVERT: J 98 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.6827 (m-80) outliers start: 96 outliers final: 53 residues processed: 248 average time/residue: 0.5099 time to fit residues: 136.8104 Evaluate side-chains 228 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.0060 chunk 108 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 90 optimal weight: 0.0570 chunk 77 optimal weight: 0.0470 chunk 94 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.2612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN L 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.212186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.196724 restraints weight = 11731.687| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.28 r_work: 0.4330 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.4227 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10565 Z= 0.113 Angle : 0.638 9.875 14369 Z= 0.324 Chirality : 0.043 0.191 1596 Planarity : 0.005 0.094 1843 Dihedral : 6.405 50.689 1493 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 5.40 % Allowed : 34.78 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 3.90 % 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: -1.20 (0.23), residues: 1304 helix: 0.34 (0.40), residues: 166 sheet: -0.56 (0.29), residues: 359 loop : -1.17 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 135 TYR 0.015 0.001 TYR J 98 PHE 0.010 0.001 PHE E 52 TRP 0.008 0.001 TRP J 51 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00266 (10549) covalent geometry : angle 0.63245 (14337) SS BOND : bond 0.00551 ( 16) SS BOND : angle 1.83945 ( 32) hydrogen bonds : bond 0.03062 ( 265) hydrogen bonds : angle 5.20984 ( 690) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.5658 (ttm-80) REVERT: A 134 ARG cc_start: 0.4962 (OUTLIER) cc_final: 0.4275 (mtp85) REVERT: C 193 ASN cc_start: 0.5981 (OUTLIER) cc_final: 0.5401 (m-40) REVERT: D 80 MET cc_start: 0.6610 (mtm) cc_final: 0.6336 (mtp) REVERT: D 82 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6251 (mp) REVERT: E 9 THR cc_start: 0.8056 (m) cc_final: 0.7841 (m) REVERT: F 14 GLU cc_start: 0.6085 (mt-10) cc_final: 0.5817 (mt-10) REVERT: F 98 CYS cc_start: 0.6776 (t) cc_final: 0.6457 (t) REVERT: B 85 THR cc_start: 0.6117 (t) cc_final: 0.5888 (t) REVERT: H 70 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.4918 (mtm-85) REVERT: H 123 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: K 53 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7041 (mp) REVERT: K 67 ARG cc_start: 0.6483 (ptp90) cc_final: 0.6073 (ptp-170) REVERT: J 98 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6770 (m-80) outliers start: 61 outliers final: 30 residues processed: 226 average time/residue: 0.4997 time to fit residues: 121.6284 Evaluate side-chains 205 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN C 128 GLN B 96 GLN L 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.210396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.194603 restraints weight = 11721.469| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.28 r_work: 0.4310 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10565 Z= 0.130 Angle : 0.669 10.917 14369 Z= 0.337 Chirality : 0.043 0.185 1596 Planarity : 0.005 0.097 1843 Dihedral : 6.287 54.171 1491 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 4.96 % Allowed : 35.49 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -1.25 (0.23), residues: 1304 helix: 0.29 (0.40), residues: 166 sheet: -0.56 (0.29), residues: 367 loop : -1.22 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.015 0.001 TYR J 98 PHE 0.017 0.002 PHE B 55 TRP 0.006 0.001 TRP B 52 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00314 (10549) covalent geometry : angle 0.66204 (14337) SS BOND : bond 0.00510 ( 16) SS BOND : angle 2.12409 ( 32) hydrogen bonds : bond 0.03214 ( 265) hydrogen bonds : angle 5.18427 ( 690) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.5137 (ttm-80) REVERT: A 134 ARG cc_start: 0.4981 (OUTLIER) cc_final: 0.4251 (mtp85) REVERT: C 193 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.5325 (m-40) REVERT: D 36 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8209 (mmtp) REVERT: D 67 MET cc_start: 0.8222 (ttt) cc_final: 0.7979 (ttt) REVERT: D 76 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7187 (mtp85) REVERT: D 82 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.6206 (mp) REVERT: F 14 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5891 (mt-10) REVERT: H 15 THR cc_start: 0.8281 (m) cc_final: 0.7992 (p) REVERT: H 70 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.4866 (mtm-85) REVERT: H 123 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7267 (mmm) REVERT: K 53 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7069 (mp) REVERT: K 67 ARG cc_start: 0.6441 (ptp90) cc_final: 0.6105 (ptp-170) REVERT: J 59 ASP cc_start: 0.3891 (p0) cc_final: 0.3666 (t0) REVERT: J 98 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6768 (m-80) outliers start: 56 outliers final: 33 residues processed: 215 average time/residue: 0.4894 time to fit residues: 113.8295 Evaluate side-chains 211 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 55 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 101 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.0570 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 169 GLN C 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.212174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.196615 restraints weight = 11659.854| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 1.26 r_work: 0.4333 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4237 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10565 Z= 0.116 Angle : 0.662 12.018 14369 Z= 0.334 Chirality : 0.043 0.183 1596 Planarity : 0.005 0.099 1843 Dihedral : 6.187 58.123 1491 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.91 % Favored : 94.94 % Rotamer: Outliers : 4.34 % Allowed : 35.93 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -1.21 (0.23), residues: 1304 helix: 0.32 (0.40), residues: 166 sheet: -0.53 (0.29), residues: 367 loop : -1.20 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 135 TYR 0.015 0.001 TYR J 98 PHE 0.011 0.001 PHE J 24 TRP 0.007 0.001 TRP B 52 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00274 (10549) covalent geometry : angle 0.66033 (14337) SS BOND : bond 0.00657 ( 16) SS BOND : angle 1.25312 ( 32) hydrogen bonds : bond 0.03083 ( 265) hydrogen bonds : angle 5.13549 ( 690) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.6488 (t80) cc_final: 0.5843 (t80) REVERT: A 65 GLU cc_start: 0.6940 (tp30) cc_final: 0.5289 (pt0) REVERT: A 79 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.5182 (ttm-80) REVERT: A 134 ARG cc_start: 0.4960 (OUTLIER) cc_final: 0.4269 (mtp85) REVERT: C 193 ASN cc_start: 0.5908 (OUTLIER) cc_final: 0.5313 (m-40) REVERT: D 36 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8125 (mmtp) REVERT: D 67 MET cc_start: 0.8229 (ttt) cc_final: 0.7960 (ttt) REVERT: D 76 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7105 (mtp85) REVERT: D 82 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6166 (mp) REVERT: F 76 ASP cc_start: 0.5344 (m-30) cc_final: 0.4969 (m-30) REVERT: H 15 THR cc_start: 0.8258 (m) cc_final: 0.7990 (p) REVERT: H 70 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.4846 (mtm-85) REVERT: H 123 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7227 (mmm) REVERT: K 53 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7046 (mp) REVERT: K 67 ARG cc_start: 0.6437 (ptp90) cc_final: 0.6176 (ptp-170) REVERT: J 98 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6755 (m-80) outliers start: 49 outliers final: 32 residues processed: 213 average time/residue: 0.4943 time to fit residues: 113.3882 Evaluate side-chains 207 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.0050 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 169 GLN C 128 GLN L 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.209438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.191231 restraints weight = 11655.069| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 1.57 r_work: 0.4251 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10565 Z= 0.131 Angle : 0.682 12.088 14369 Z= 0.346 Chirality : 0.043 0.198 1596 Planarity : 0.005 0.100 1843 Dihedral : 6.186 53.482 1490 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 4.60 % Allowed : 35.84 % Favored : 59.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -1.20 (0.23), residues: 1304 helix: 0.17 (0.39), residues: 166 sheet: -0.53 (0.29), residues: 367 loop : -1.15 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.015 0.001 TYR J 98 PHE 0.017 0.002 PHE B 55 TRP 0.007 0.001 TRP B 52 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00309 (10549) covalent geometry : angle 0.67947 (14337) SS BOND : bond 0.00521 ( 16) SS BOND : angle 1.41821 ( 32) hydrogen bonds : bond 0.03185 ( 265) hydrogen bonds : angle 5.14969 ( 690) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 TYR cc_start: 0.6563 (t80) cc_final: 0.5776 (t80) REVERT: A 65 GLU cc_start: 0.7018 (tp30) cc_final: 0.5123 (pt0) REVERT: A 79 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5137 (ttm-80) REVERT: A 134 ARG cc_start: 0.5021 (OUTLIER) cc_final: 0.4138 (mtp85) REVERT: A 169 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6957 (pt0) REVERT: C 193 ASN cc_start: 0.5879 (OUTLIER) cc_final: 0.5300 (m-40) REVERT: D 36 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8065 (mmtp) REVERT: D 67 MET cc_start: 0.8215 (ttt) cc_final: 0.7923 (ttt) REVERT: D 76 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7155 (mtp85) REVERT: D 82 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6138 (mp) REVERT: B 145 MET cc_start: 0.6342 (tpt) cc_final: 0.5285 (ttp) REVERT: H 15 THR cc_start: 0.8405 (m) cc_final: 0.8067 (p) REVERT: H 70 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.4739 (mtm-85) REVERT: K 53 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6977 (mp) REVERT: K 67 ARG cc_start: 0.6371 (ptp90) cc_final: 0.6013 (ptp-170) REVERT: J 98 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6655 (m-80) outliers start: 52 outliers final: 35 residues processed: 209 average time/residue: 0.5159 time to fit residues: 116.5185 Evaluate side-chains 208 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain H residue 70 ARG Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain L residue 17 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 PHE Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 42 ARG Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 101 HIS Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 169 GLN C 128 GLN F 13 GLN L 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.203944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.184769 restraints weight = 11980.192| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 1.64 r_work: 0.4192 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10565 Z= 0.189 Angle : 0.760 11.820 14369 Z= 0.386 Chirality : 0.046 0.211 1596 Planarity : 0.006 0.101 1843 Dihedral : 6.427 51.843 1490 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.83 % Favored : 94.02 % Rotamer: Outliers : 4.87 % Allowed : 35.84 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 2.60 % 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: -1.34 (0.23), residues: 1304 helix: -0.07 (0.39), residues: 163 sheet: -0.63 (0.29), residues: 367 loop : -1.20 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.020 0.002 TYR B 184 PHE 0.017 0.002 PHE E 52 TRP 0.013 0.001 TRP F 52 HIS 0.013 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00452 (10549) covalent geometry : angle 0.75614 (14337) SS BOND : bond 0.00686 ( 16) SS BOND : angle 1.79582 ( 32) hydrogen bonds : bond 0.03813 ( 265) hydrogen bonds : angle 5.36531 ( 690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.17 seconds wall clock time: 63 minutes 24.36 seconds (3804.36 seconds total)