Starting phenix.real_space_refine on Wed Feb 4 10:24:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3k_47486/02_2026/9e3k_47486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3k_47486/02_2026/9e3k_47486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3k_47486/02_2026/9e3k_47486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3k_47486/02_2026/9e3k_47486.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3k_47486/02_2026/9e3k_47486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3k_47486/02_2026/9e3k_47486.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 65 5.16 5 C 6326 2.51 5 N 1725 2.21 5 O 1905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 10021 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: "B" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 801 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1509 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 184} 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: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "K" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 807 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "J" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 2.25, per 1000 atoms: 0.22 Number of scatterers: 10021 At special positions: 0 Unit cell: (90.2, 97.58, 151.7, 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 65 16.00 O 1905 8.00 N 1725 7.00 C 6326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 201 " distance=2.03 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 C 23 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 134 " distance=2.02 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 199 " distance=2.03 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 41 " distance=2.05 Simple disulfide: pdb=" SG CYS F 92 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 107 " 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: 0.87 Conformation dependent library (CDL) restraints added in 383.1 milliseconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 17.7% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 4.356A pdb=" N GLN A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 56 through 77 removed outlier: 3.567A pdb=" N THR A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.580A pdb=" N GLY A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.927A pdb=" N GLY A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (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 205 Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.215A pdb=" N TYR A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 160 removed outlier: 4.411A pdb=" N LYS B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N MET B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 38 through 47 removed outlier: 4.205A pdb=" N GLN C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 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: 4.051A pdb=" N ARG C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 159 " --> pdb=" O MET C 155 " (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: 3.529A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 removed outlier: 3.760A pdb=" N MET E 67 " --> pdb=" O PRO E 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 67 removed outlier: 3.686A pdb=" N PHE F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.537A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.888A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.575A pdb=" N SER L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.317A pdb=" N ASN J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP J 32 " --> pdb=" O ILE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.535A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 11 removed outlier: 3.911A pdb=" N ARG A 143 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG A 92 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 141 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 150 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 155 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 114 removed outlier: 5.837A pdb=" N ALA B 108 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 124 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG B 110 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 122 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 5.683A 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 191 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 191 current: chain 'C' and resid 119 through 125 removed outlier: 3.540A pdb=" N ILE C 131 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG C 125 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 128 through 135 current: chain 'C' and resid 183 through 191 removed outlier: 9.736A pdb=" N THR C 187 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL D 16 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE D 33 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL D 16 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS D 31 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET D 18 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU D 29 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 8.455A 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 26 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 38 through 40 current: chain 'F' and resid 85 through 91 Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.617A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.892A pdb=" N ALA K 35 " --> pdb=" O GLN K 90 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 5.983A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.555A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.585A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL J 37 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA J 33 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 23 275 hydrogen bonds defined for protein. 711 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: 1.47 Time building geometry restraints manager: 1.15 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: 3261 1.35 - 1.48: 2715 1.48 - 1.61: 4177 1.61 - 1.74: 1 1.74 - 1.87: 94 Bond restraints: 10248 Sorted by residual: bond pdb=" CB PRO K 41 " pdb=" CG PRO K 41 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.76e+00 bond pdb=" CA ILE B 131 " pdb=" CB ILE B 131 " ideal model delta sigma weight residual 1.553 1.539 0.014 7.40e-03 1.83e+04 3.82e+00 bond pdb=" CB CYS F 27 " pdb=" SG CYS F 27 " ideal model delta sigma weight residual 1.808 1.872 -0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG PRO K 41 " pdb=" CD PRO K 41 " ideal model delta sigma weight residual 1.503 1.557 -0.054 3.40e-02 8.65e+02 2.49e+00 bond pdb=" CB GLU H 6 " pdb=" CG GLU H 6 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 10243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13644 1.94 - 3.87: 222 3.87 - 5.81: 34 5.81 - 7.75: 9 7.75 - 9.69: 6 Bond angle restraints: 13915 Sorted by residual: angle pdb=" CA PRO K 41 " pdb=" N PRO K 41 " pdb=" CD PRO K 41 " ideal model delta sigma weight residual 112.00 102.36 9.64 1.40e+00 5.10e-01 4.74e+01 angle pdb=" N CYS F 41 " pdb=" CA CYS F 41 " pdb=" C CYS F 41 " ideal model delta sigma weight residual 107.93 117.14 -9.21 1.65e+00 3.67e-01 3.11e+01 angle pdb=" CA CYS F 41 " pdb=" CB CYS F 41 " pdb=" SG CYS F 41 " ideal model delta sigma weight residual 114.40 124.09 -9.69 2.30e+00 1.89e-01 1.77e+01 angle pdb=" C ASP J 118 " pdb=" CA ASP J 118 " pdb=" CB ASP J 118 " ideal model delta sigma weight residual 110.06 105.98 4.08 1.44e+00 4.82e-01 8.04e+00 angle pdb=" N SER L 7 " pdb=" CA SER L 7 " pdb=" C SER L 7 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.74e+00 ... (remaining 13910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5274 17.89 - 35.79: 641 35.79 - 53.68: 194 53.68 - 71.57: 32 71.57 - 89.47: 13 Dihedral angle restraints: 6154 sinusoidal: 2398 harmonic: 3756 Sorted by residual: dihedral pdb=" CA GLY K 51 " pdb=" C GLY K 51 " pdb=" N ALA K 52 " pdb=" CA ALA K 52 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 137.04 -44.04 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CB CYS F 27 " pdb=" SG CYS F 27 " pdb=" SG CYS F 41 " pdb=" CB CYS F 41 " ideal model delta sinusoidal sigma weight residual 93.00 49.76 43.24 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 6151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1280 0.056 - 0.112: 220 0.112 - 0.167: 32 0.167 - 0.223: 1 0.223 - 0.279: 1 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA CYS F 41 " pdb=" N CYS F 41 " pdb=" C CYS F 41 " pdb=" CB CYS F 41 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU E 78 " pdb=" CB LEU E 78 " pdb=" CD1 LEU E 78 " pdb=" CD2 LEU E 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA PRO H 14 " pdb=" N PRO H 14 " pdb=" C PRO H 14 " pdb=" CB PRO H 14 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1531 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 40 " 0.080 5.00e-02 4.00e+02 1.14e-01 2.08e+01 pdb=" N PRO K 41 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO K 41 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO K 41 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 7 " -0.065 5.00e-02 4.00e+02 9.85e-02 1.55e+01 pdb=" N PRO K 8 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO K 8 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO K 8 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 52 " -0.027 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP F 52 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP F 52 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 52 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP F 52 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 52 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 52 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 52 " -0.001 2.00e-02 2.50e+03 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 187 2.66 - 3.22: 9050 3.22 - 3.78: 15149 3.78 - 4.34: 20978 4.34 - 4.90: 34929 Nonbonded interactions: 80293 Sorted by model distance: nonbonded pdb=" O ARG C 110 " pdb=" OH TYR C 176 " model vdw 2.106 3.040 nonbonded pdb=" OD1 ASN C 25 " pdb=" OG1 THR C 115 " model vdw 2.178 3.040 nonbonded pdb=" O ARG B 110 " pdb=" OH TYR B 176 " model vdw 2.193 3.040 nonbonded pdb=" O ARG A 92 " pdb=" ND2 ASN A 140 " model vdw 2.206 3.120 nonbonded pdb=" O PRO C 24 " pdb=" OG1 THR C 27 " model vdw 2.215 3.040 ... (remaining 80288 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' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 107)) } 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.060 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.004 0.120 10266 Z= 0.179 Angle : 0.656 9.685 13951 Z= 0.334 Chirality : 0.044 0.279 1534 Planarity : 0.006 0.114 1795 Dihedral : 17.142 89.467 3720 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.37 % Allowed : 29.36 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1278 helix: -0.95 (0.40), residues: 146 sheet: -0.68 (0.25), residues: 464 loop : -0.84 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.012 0.001 TYR A 166 PHE 0.019 0.002 PHE F 53 TRP 0.055 0.002 TRP F 52 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00424 (10248) covalent geometry : angle 0.65206 (13915) SS BOND : bond 0.00551 ( 18) SS BOND : angle 1.48749 ( 36) hydrogen bonds : bond 0.25614 ( 275) hydrogen bonds : angle 9.86868 ( 711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 0.377 Fit side-chains REVERT: A 13 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8058 (mtm-85) REVERT: H 59 TYR cc_start: 0.8459 (m-80) cc_final: 0.8058 (m-80) REVERT: J 60 TYR cc_start: 0.8408 (m-80) cc_final: 0.7918 (m-80) outliers start: 4 outliers final: 2 residues processed: 200 average time/residue: 0.1202 time to fit residues: 32.3578 Evaluate side-chains 198 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 57 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0010 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.137558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125334 restraints weight = 14480.797| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.19 r_work: 0.3522 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10266 Z= 0.112 Angle : 0.599 8.289 13951 Z= 0.303 Chirality : 0.042 0.166 1534 Planarity : 0.006 0.061 1795 Dihedral : 4.669 57.522 1468 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.63 % Allowed : 25.72 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.23), residues: 1278 helix: 0.08 (0.43), residues: 149 sheet: -0.48 (0.25), residues: 458 loop : -0.71 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 13 TYR 0.025 0.001 TYR K 50 PHE 0.012 0.001 PHE E 52 TRP 0.037 0.001 TRP F 52 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00261 (10248) covalent geometry : angle 0.59717 (13915) SS BOND : bond 0.00293 ( 18) SS BOND : angle 1.05962 ( 36) hydrogen bonds : bond 0.04465 ( 275) hydrogen bonds : angle 6.51498 ( 711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 150 ASN cc_start: 0.7274 (t0) cc_final: 0.6982 (t0) REVERT: B 143 TRP cc_start: 0.7672 (p-90) cc_final: 0.7447 (p-90) REVERT: C 72 LYS cc_start: 0.8197 (ttpp) cc_final: 0.7966 (ttpp) REVERT: E 102 GLU cc_start: 0.7755 (tt0) cc_final: 0.7548 (tt0) REVERT: L 18 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7402 (ttm170) REVERT: J 60 TYR cc_start: 0.8336 (m-80) cc_final: 0.7672 (m-80) outliers start: 39 outliers final: 17 residues processed: 218 average time/residue: 0.1151 time to fit residues: 34.3328 Evaluate side-chains 200 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 114 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN K 6 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122809 restraints weight = 14402.740| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.16 r_work: 0.3489 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10266 Z= 0.168 Angle : 0.602 9.157 13951 Z= 0.304 Chirality : 0.043 0.176 1534 Planarity : 0.005 0.061 1795 Dihedral : 4.850 59.066 1465 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.66 % Allowed : 24.88 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1278 helix: 0.28 (0.43), residues: 152 sheet: -0.35 (0.24), residues: 459 loop : -0.82 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 13 TYR 0.028 0.001 TYR K 50 PHE 0.014 0.002 PHE E 52 TRP 0.030 0.002 TRP F 52 HIS 0.005 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00392 (10248) covalent geometry : angle 0.59997 (13915) SS BOND : bond 0.00376 ( 18) SS BOND : angle 1.20535 ( 36) hydrogen bonds : bond 0.03990 ( 275) hydrogen bonds : angle 5.94875 ( 711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8046 (mtm-85) REVERT: B 143 TRP cc_start: 0.7696 (p-90) cc_final: 0.7433 (p-90) REVERT: C 36 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7357 (ttp-170) REVERT: C 72 LYS cc_start: 0.8263 (ttpp) cc_final: 0.8040 (ttpp) REVERT: L 18 ARG cc_start: 0.7741 (ttm170) cc_final: 0.7297 (ttt180) outliers start: 50 outliers final: 26 residues processed: 232 average time/residue: 0.1106 time to fit residues: 35.5002 Evaluate side-chains 222 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 122 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 140 ASN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN E 75 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 122 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122407 restraints weight = 14650.906| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.18 r_work: 0.3480 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10266 Z= 0.177 Angle : 0.607 8.182 13951 Z= 0.305 Chirality : 0.043 0.182 1534 Planarity : 0.005 0.063 1795 Dihedral : 4.901 58.996 1465 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.47 % Allowed : 24.79 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1278 helix: 0.39 (0.42), residues: 152 sheet: -0.37 (0.24), residues: 469 loop : -0.84 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 27 TYR 0.028 0.001 TYR K 50 PHE 0.015 0.002 PHE E 52 TRP 0.021 0.002 TRP F 52 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00414 (10248) covalent geometry : angle 0.60371 (13915) SS BOND : bond 0.00389 ( 18) SS BOND : angle 1.33893 ( 36) hydrogen bonds : bond 0.03591 ( 275) hydrogen bonds : angle 5.79352 ( 711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.8024 (mtm-85) REVERT: B 143 TRP cc_start: 0.7674 (p-90) cc_final: 0.7419 (p-90) REVERT: C 36 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7345 (ttp-170) REVERT: C 72 LYS cc_start: 0.8269 (ttpp) cc_final: 0.7980 (ttpp) REVERT: C 169 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8454 (mttt) REVERT: L 18 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7296 (ttt180) REVERT: J 60 TYR cc_start: 0.8348 (m-80) cc_final: 0.7681 (m-80) outliers start: 48 outliers final: 32 residues processed: 232 average time/residue: 0.1178 time to fit residues: 37.2595 Evaluate side-chains 229 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 122 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 104 optimal weight: 0.0040 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123319 restraints weight = 14628.021| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.27 r_work: 0.3496 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10266 Z= 0.151 Angle : 0.590 7.836 13951 Z= 0.297 Chirality : 0.042 0.170 1534 Planarity : 0.005 0.064 1795 Dihedral : 4.889 59.399 1465 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.29 % Allowed : 25.26 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1278 helix: 0.48 (0.42), residues: 150 sheet: -0.40 (0.24), residues: 468 loop : -0.79 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.029 0.001 TYR K 50 PHE 0.013 0.001 PHE E 52 TRP 0.020 0.002 TRP F 52 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00358 (10248) covalent geometry : angle 0.58882 (13915) SS BOND : bond 0.00338 ( 18) SS BOND : angle 1.01691 ( 36) hydrogen bonds : bond 0.03348 ( 275) hydrogen bonds : angle 5.64955 ( 711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.8036 (mtm-85) REVERT: A 30 ASP cc_start: 0.8518 (p0) cc_final: 0.8131 (p0) REVERT: B 143 TRP cc_start: 0.7698 (p-90) cc_final: 0.7427 (p-90) REVERT: C 36 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7322 (ttp-170) REVERT: C 157 TYR cc_start: 0.8153 (t80) cc_final: 0.7891 (t80) REVERT: C 169 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8423 (mttt) REVERT: K 90 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: L 18 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7268 (ttt180) outliers start: 46 outliers final: 31 residues processed: 225 average time/residue: 0.1059 time to fit residues: 32.6519 Evaluate side-chains 223 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 108 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123198 restraints weight = 14729.619| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.26 r_work: 0.3488 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10266 Z= 0.162 Angle : 0.587 8.941 13951 Z= 0.296 Chirality : 0.042 0.170 1534 Planarity : 0.005 0.064 1795 Dihedral : 4.941 60.952 1465 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.94 % Allowed : 24.98 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.23), residues: 1278 helix: 0.57 (0.43), residues: 150 sheet: -0.38 (0.24), residues: 468 loop : -0.82 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 76 TYR 0.032 0.001 TYR K 50 PHE 0.014 0.001 PHE E 52 TRP 0.023 0.002 TRP F 52 HIS 0.004 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00384 (10248) covalent geometry : angle 0.58576 (13915) SS BOND : bond 0.00375 ( 18) SS BOND : angle 1.03473 ( 36) hydrogen bonds : bond 0.03288 ( 275) hydrogen bonds : angle 5.53395 ( 711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.8019 (mtm-85) REVERT: A 30 ASP cc_start: 0.8535 (p0) cc_final: 0.8143 (p0) REVERT: A 39 ARG cc_start: 0.8551 (mmm160) cc_final: 0.8340 (mmm160) REVERT: B 143 TRP cc_start: 0.7735 (p-90) cc_final: 0.7476 (p-90) REVERT: C 36 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7283 (ttp-170) REVERT: C 169 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: F 88 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7170 (tm-30) REVERT: L 18 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7301 (ttt180) REVERT: J 60 TYR cc_start: 0.8346 (m-80) cc_final: 0.7564 (m-80) outliers start: 53 outliers final: 39 residues processed: 238 average time/residue: 0.1052 time to fit residues: 34.5333 Evaluate side-chains 243 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN K 90 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123043 restraints weight = 14557.107| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.24 r_work: 0.3486 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10266 Z= 0.161 Angle : 0.594 8.366 13951 Z= 0.298 Chirality : 0.042 0.176 1534 Planarity : 0.005 0.067 1795 Dihedral : 4.946 61.826 1465 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.03 % Allowed : 25.44 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1278 helix: 0.71 (0.43), residues: 150 sheet: -0.37 (0.24), residues: 467 loop : -0.84 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 76 TYR 0.027 0.001 TYR K 50 PHE 0.014 0.001 PHE E 52 TRP 0.024 0.002 TRP F 52 HIS 0.004 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00379 (10248) covalent geometry : angle 0.59154 (13915) SS BOND : bond 0.00392 ( 18) SS BOND : angle 1.12470 ( 36) hydrogen bonds : bond 0.03281 ( 275) hydrogen bonds : angle 5.49465 ( 711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8257 (mtm-85) cc_final: 0.7985 (mtm-85) REVERT: A 30 ASP cc_start: 0.8543 (p0) cc_final: 0.8156 (p0) REVERT: A 60 THR cc_start: 0.7282 (p) cc_final: 0.7073 (p) REVERT: B 143 TRP cc_start: 0.7711 (p-90) cc_final: 0.7456 (p-90) REVERT: C 36 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7267 (ttp-170) REVERT: C 62 TYR cc_start: 0.7603 (t80) cc_final: 0.7388 (t80) REVERT: C 169 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8414 (mttt) REVERT: E 102 GLU cc_start: 0.7842 (tt0) cc_final: 0.7625 (tt0) REVERT: F 88 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7169 (tm-30) REVERT: L 18 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7354 (ttt180) REVERT: J 60 TYR cc_start: 0.8343 (m-80) cc_final: 0.7563 (m-80) REVERT: J 107 CYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7113 (m) outliers start: 54 outliers final: 39 residues processed: 235 average time/residue: 0.1091 time to fit residues: 35.2000 Evaluate side-chains 239 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122243 restraints weight = 14568.223| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.22 r_work: 0.3472 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10266 Z= 0.202 Angle : 0.621 10.306 13951 Z= 0.312 Chirality : 0.044 0.188 1534 Planarity : 0.005 0.068 1795 Dihedral : 5.022 62.605 1465 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.94 % Allowed : 25.35 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1278 helix: 0.64 (0.43), residues: 150 sheet: -0.39 (0.25), residues: 465 loop : -0.88 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 76 TYR 0.031 0.001 TYR K 50 PHE 0.016 0.002 PHE E 52 TRP 0.022 0.002 TRP F 52 HIS 0.005 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00472 (10248) covalent geometry : angle 0.61781 (13915) SS BOND : bond 0.00565 ( 18) SS BOND : angle 1.44609 ( 36) hydrogen bonds : bond 0.03431 ( 275) hydrogen bonds : angle 5.56137 ( 711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: A 30 ASP cc_start: 0.8539 (p0) cc_final: 0.8154 (p0) REVERT: B 143 TRP cc_start: 0.7727 (p-90) cc_final: 0.7460 (p-90) REVERT: C 36 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7231 (ttp-170) REVERT: C 62 TYR cc_start: 0.7619 (t80) cc_final: 0.7399 (t80) REVERT: C 139 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: C 169 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8417 (mttt) REVERT: D 67 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7108 (ttp) REVERT: F 88 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7192 (tm-30) REVERT: L 18 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7417 (ttt180) REVERT: J 60 TYR cc_start: 0.8351 (m-80) cc_final: 0.7554 (m-80) REVERT: J 107 CYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7181 (m) outliers start: 53 outliers final: 41 residues processed: 236 average time/residue: 0.1079 time to fit residues: 35.0602 Evaluate side-chains 245 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122117 restraints weight = 14573.046| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.23 r_work: 0.3469 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10266 Z= 0.203 Angle : 0.635 10.050 13951 Z= 0.319 Chirality : 0.044 0.179 1534 Planarity : 0.005 0.071 1795 Dihedral : 5.089 62.666 1465 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.29 % Allowed : 26.84 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1278 helix: 0.68 (0.43), residues: 150 sheet: -0.43 (0.25), residues: 467 loop : -0.92 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 76 TYR 0.029 0.001 TYR K 50 PHE 0.016 0.002 PHE E 52 TRP 0.022 0.002 TRP F 52 HIS 0.007 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00477 (10248) covalent geometry : angle 0.63154 (13915) SS BOND : bond 0.00535 ( 18) SS BOND : angle 1.45036 ( 36) hydrogen bonds : bond 0.03417 ( 275) hydrogen bonds : angle 5.58776 ( 711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7994 (mtm-85) REVERT: A 30 ASP cc_start: 0.8539 (p0) cc_final: 0.8160 (p0) REVERT: B 143 TRP cc_start: 0.7735 (p-90) cc_final: 0.7483 (p-90) REVERT: C 62 TYR cc_start: 0.7629 (t80) cc_final: 0.7404 (t80) REVERT: C 139 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: C 142 TYR cc_start: 0.8519 (m-80) cc_final: 0.8217 (m-80) REVERT: C 149 LEU cc_start: 0.8342 (mt) cc_final: 0.8020 (mp) REVERT: C 169 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8415 (mttt) REVERT: D 67 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7094 (ttp) REVERT: F 88 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7182 (tm-30) REVERT: L 18 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7429 (ttt180) REVERT: J 60 TYR cc_start: 0.8352 (m-80) cc_final: 0.7609 (m-80) REVERT: J 107 CYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7201 (m) outliers start: 46 outliers final: 39 residues processed: 227 average time/residue: 0.1077 time to fit residues: 33.8385 Evaluate side-chains 238 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123230 restraints weight = 14497.667| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.23 r_work: 0.3492 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10266 Z= 0.137 Angle : 0.601 10.105 13951 Z= 0.299 Chirality : 0.043 0.181 1534 Planarity : 0.005 0.069 1795 Dihedral : 4.978 62.429 1465 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.38 % Allowed : 26.00 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1278 helix: 0.78 (0.43), residues: 150 sheet: -0.40 (0.24), residues: 465 loop : -0.87 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 76 TYR 0.030 0.001 TYR K 50 PHE 0.013 0.001 PHE E 52 TRP 0.024 0.001 TRP F 52 HIS 0.006 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (10248) covalent geometry : angle 0.59816 (13915) SS BOND : bond 0.00482 ( 18) SS BOND : angle 1.28205 ( 36) hydrogen bonds : bond 0.03099 ( 275) hydrogen bonds : angle 5.44724 ( 711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7977 (mtm-85) REVERT: A 30 ASP cc_start: 0.8540 (p0) cc_final: 0.8163 (p0) REVERT: A 37 THR cc_start: 0.7952 (m) cc_final: 0.7743 (m) REVERT: B 143 TRP cc_start: 0.7722 (p-90) cc_final: 0.7468 (p-90) REVERT: C 36 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7182 (ttp-170) REVERT: C 62 TYR cc_start: 0.7602 (t80) cc_final: 0.7369 (t80) REVERT: C 139 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: C 149 LEU cc_start: 0.8262 (mt) cc_final: 0.7944 (mp) REVERT: C 169 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8379 (mttt) REVERT: D 67 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7066 (ttp) REVERT: E 73 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7165 (mpp) REVERT: E 102 GLU cc_start: 0.7867 (tt0) cc_final: 0.7600 (tt0) REVERT: F 88 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7167 (tm-30) REVERT: L 18 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7363 (ttt180) REVERT: J 37 VAL cc_start: 0.7929 (t) cc_final: 0.7718 (t) REVERT: J 60 TYR cc_start: 0.8342 (m-80) cc_final: 0.7545 (m-80) REVERT: J 107 CYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7136 (m) outliers start: 47 outliers final: 36 residues processed: 221 average time/residue: 0.1045 time to fit residues: 31.6672 Evaluate side-chains 236 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122752 restraints weight = 14611.636| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.24 r_work: 0.3481 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10266 Z= 0.166 Angle : 0.614 9.678 13951 Z= 0.307 Chirality : 0.043 0.215 1534 Planarity : 0.005 0.070 1795 Dihedral : 5.030 65.334 1465 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.19 % Allowed : 26.37 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.23), residues: 1278 helix: 0.78 (0.44), residues: 150 sheet: -0.40 (0.24), residues: 463 loop : -0.87 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.029 0.001 TYR K 50 PHE 0.014 0.002 PHE E 52 TRP 0.023 0.002 TRP F 52 HIS 0.014 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00392 (10248) covalent geometry : angle 0.61114 (13915) SS BOND : bond 0.00495 ( 18) SS BOND : angle 1.32857 ( 36) hydrogen bonds : bond 0.03219 ( 275) hydrogen bonds : angle 5.46518 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.95 seconds wall clock time: 47 minutes 3.74 seconds (2823.74 seconds total)