Starting phenix.real_space_refine on Sat Jul 4 18:22:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.cif" model { file = "/net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8der_27396/07_2026/8der_27396.map" } resolution = 3.3 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= 0.002 sd= 0.031 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 135 5.16 5 C 14269 2.51 5 N 3899 2.21 5 O 4362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22665 Number of models: 1 Model: "" Number of chains: 18 Chain: "X" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Y" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3068 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "E" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3068 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2707 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 320} Chain: "F" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3068 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2707 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 320} Chain: "A" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2699 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.88, per 1000 atoms: 0.22 Number of scatterers: 22665 At special positions: 0 Unit cell: (169.32, 165.585, 158.115, 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 135 16.00 O 4362 8.00 N 3899 7.00 C 14269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.04 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 266 " distance=2.04 Simple disulfide: pdb=" SG CYS C 200 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 202 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.02 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 27 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 226 " distance=2.02 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.06 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG D 1 " - " ASN C 212 " " NAG E 501 " - " ASN E 134 " " NAG F 501 " - " ASN F 134 " " NAG G 501 " - " ASN G 134 " " NAG I 1 " - " ASN B 212 " " NAG J 1 " - " ASN A 212 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5386 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 79 sheets defined 6.3% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'X' and resid 28 through 32 removed outlier: 3.550A pdb=" N PHE X 32 " --> pdb=" O PHE X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.393A pdb=" N LEU G 115 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.731A pdb=" N VAL G 159 " --> pdb=" O PHE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.912A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.667A pdb=" N PHE G 287 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 256 through 259 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.695A pdb=" N PHE C 6 " --> pdb=" O THR C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'F' and resid 238 through 247 Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 256 through 259 Processing helix chain 'F' and resid 283 through 287 removed outlier: 4.022A pdb=" N PHE F 287 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 293 Processing helix chain 'B' and resid 1 through 6 removed outlier: 4.021A pdb=" N GLU B 4 " --> pdb=" O SER B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.759A pdb=" N PHE A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.630A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'W' and resid 28 through 32 removed outlier: 3.968A pdb=" N ASP W 31 " --> pdb=" O ARG W 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE W 32 " --> pdb=" O PHE W 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 28 through 32' Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'V' and resid 27 through 31 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.775A pdb=" N GLU V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.715A pdb=" N MET X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.762A pdb=" N CYS X 92 " --> pdb=" O TRP X 103 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP X 103 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG X 94 " --> pdb=" O ASP X 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 9 through 12 removed outlier: 5.845A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'Y' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 15 through 21 removed outlier: 5.381A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 140 through 148 removed outlier: 4.340A pdb=" N VAL G 129 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AB2, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'G' and resid 203 through 204 removed outlier: 3.548A pdb=" N TYR G 214 " --> pdb=" O GLN G 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AB6, first strand: chain 'G' and resid 296 through 305 removed outlier: 6.328A pdb=" N ALA G 299 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER G 321 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N CYS G 301 " --> pdb=" O LYS G 319 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS G 319 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU G 303 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR G 317 " --> pdb=" O LEU G 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AB9, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AC1, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC2, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.415A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 140 through 148 removed outlier: 4.391A pdb=" N VAL E 129 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AC7, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AC8, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AC9, first strand: chain 'E' and resid 297 through 306 removed outlier: 5.971A pdb=" N ALA E 299 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER E 321 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS E 301 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS E 319 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 303 " --> pdb=" O THR E 317 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR E 317 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AD2, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AD3, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AD4, first strand: chain 'C' and resid 33 through 40 removed outlier: 8.295A pdb=" N ILE C 33 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER C 50 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 35 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 39 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N SER C 50 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP C 69 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR C 65 " --> pdb=" O GLY C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 40 removed outlier: 8.295A pdb=" N ILE C 33 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER C 50 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 35 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 39 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR C 98 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N SER C 51 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS C 96 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N TYR C 53 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N ASP C 94 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 14.232A pdb=" N LEU C 55 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 16.997A pdb=" N ILE C 92 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 147 through 154 Processing sheet with id=AD8, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=AD9, first strand: chain 'C' and resid 173 through 174 removed outlier: 3.583A pdb=" N GLU C 173 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AE2, first strand: chain 'C' and resid 275 through 279 Processing sheet with id=AE3, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AE4, first strand: chain 'F' and resid 15 through 21 removed outlier: 3.831A pdb=" N LEU F 27 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG F 21 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE F 31 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN F 134 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR F 126 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN F 43 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA F 124 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU F 45 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR F 122 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 47 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU F 120 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 143 through 147 removed outlier: 6.816A pdb=" N GLU F 120 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 47 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR F 122 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU F 45 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA F 124 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN F 43 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR F 126 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN F 134 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE F 31 " --> pdb=" O THR F 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 51 through 61 removed outlier: 4.678A pdb=" N LYS F 105 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL F 103 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 60 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR F 101 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'F' and resid 203 through 205 Processing sheet with id=AE9, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AF1, first strand: chain 'F' and resid 300 through 306 removed outlier: 6.518A pdb=" N ILE F 315 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 326 through 329 removed outlier: 3.524A pdb=" N CYS F 328 " --> pdb=" O VAL F 344 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 364 through 368 Processing sheet with id=AF4, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AF5, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AF6, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.517A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N SER B 50 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP B 69 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR B 65 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.517A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR B 98 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N SER B 51 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N HIS B 96 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N TYR B 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N ASP B 94 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 14.595A pdb=" N LEU B 55 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 17.227A pdb=" N ILE B 92 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AF9, first strand: chain 'B' and resid 147 through 154 Processing sheet with id=AG1, first strand: chain 'B' and resid 237 through 238 removed outlier: 3.821A pdb=" N GLY B 253 " --> pdb=" O MET B 167 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.878A pdb=" N GLU B 173 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 195 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS B 202 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 179 through 182 removed outlier: 3.952A pdb=" N VAL B 186 " --> pdb=" O PHE B 217 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AG5, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AG6, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.590A pdb=" N ALA A 35 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY A 95 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 101 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 65 through 70 Processing sheet with id=AG8, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AG9, first strand: chain 'A' and resid 147 through 154 Processing sheet with id=AH1, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AH2, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.997A pdb=" N GLU A 173 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 195 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.882A pdb=" N VAL A 186 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 275 through 279 Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.346A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.715A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.534A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.534A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AI2, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'W' and resid 11 through 12 removed outlier: 6.656A pdb=" N MET W 34 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'W' and resid 11 through 12 removed outlier: 6.555A pdb=" N CYS W 92 " --> pdb=" O TRP W 103 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP W 103 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG W 94 " --> pdb=" O ASP W 101 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.293A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP V 35 " --> pdb=" O VAL V 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.293A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 19 through 24 839 hydrogen bonds defined for protein. 1992 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: 4.04 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7364 1.34 - 1.47: 5729 1.47 - 1.59: 9997 1.59 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 23264 Sorted by residual: bond pdb=" N PRO F 333 " pdb=" CD PRO F 333 " ideal model delta sigma weight residual 1.473 1.421 0.052 1.40e-02 5.10e+03 1.36e+01 bond pdb=" N CYS F 328 " pdb=" CA CYS F 328 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" N GLN F 349 " pdb=" CA GLN F 349 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.08e-02 8.57e+03 9.84e+00 bond pdb=" CA SER W 100C" pdb=" CB SER W 100C" ideal model delta sigma weight residual 1.534 1.478 0.056 1.78e-02 3.16e+03 9.82e+00 bond pdb=" N VAL C 119 " pdb=" CA VAL C 119 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.29e-02 6.01e+03 9.60e+00 ... (remaining 23259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 30789 2.33 - 4.67: 809 4.67 - 7.00: 59 7.00 - 9.33: 3 9.33 - 11.67: 3 Bond angle restraints: 31663 Sorted by residual: angle pdb=" C THR F 371 " pdb=" N SER F 372 " pdb=" CA SER F 372 " ideal model delta sigma weight residual 122.53 112.54 9.99 1.61e+00 3.86e-01 3.85e+01 angle pdb=" N PRO W 97 " pdb=" CA PRO W 97 " pdb=" C PRO W 97 " ideal model delta sigma weight residual 113.53 105.83 7.70 1.39e+00 5.18e-01 3.07e+01 angle pdb=" N ILE F 361 " pdb=" CA ILE F 361 " pdb=" C ILE F 361 " ideal model delta sigma weight residual 110.62 105.57 5.05 1.02e+00 9.61e-01 2.45e+01 angle pdb=" N ASN C 212 " pdb=" CA ASN C 212 " pdb=" C ASN C 212 " ideal model delta sigma weight residual 113.30 106.94 6.36 1.34e+00 5.57e-01 2.25e+01 angle pdb=" CA GLY W 106 " pdb=" C GLY W 106 " pdb=" O GLY W 106 " ideal model delta sigma weight residual 121.88 118.24 3.64 7.80e-01 1.64e+00 2.17e+01 ... (remaining 31658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12852 17.98 - 35.96: 813 35.96 - 53.94: 154 53.94 - 71.91: 30 71.91 - 89.89: 16 Dihedral angle restraints: 13865 sinusoidal: 5432 harmonic: 8433 Sorted by residual: dihedral pdb=" CB CYS E 328 " pdb=" SG CYS E 328 " pdb=" SG CYS E 370 " pdb=" CB CYS E 370 " ideal model delta sinusoidal sigma weight residual 93.00 151.18 -58.18 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS G 63 " pdb=" SG CYS G 63 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.29 48.71 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS E 301 " pdb=" SG CYS E 301 " pdb=" SG CYS E 376 " pdb=" CB CYS E 376 " ideal model delta sinusoidal sigma weight residual -86.00 -38.42 -47.58 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 13862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3398 0.133 - 0.267: 85 0.267 - 0.400: 5 0.400 - 0.533: 1 0.533 - 0.667: 1 Chirality restraints: 3490 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.25e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 212 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 3487 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 501 " -0.326 2.00e-02 2.50e+03 2.76e-01 9.52e+02 pdb=" C7 NAG G 501 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG G 501 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG G 501 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG G 501 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.316 2.00e-02 2.50e+03 2.69e-01 9.06e+02 pdb=" C7 NAG E 501 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.213 2.00e-02 2.50e+03 1.76e-01 3.89e+02 pdb=" C7 NAG I 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.289 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.018 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 138 2.55 - 3.14: 17778 3.14 - 3.73: 32978 3.73 - 4.31: 47899 4.31 - 4.90: 82124 Nonbonded interactions: 180917 Sorted by model distance: nonbonded pdb=" OG1 THR B 297 " pdb=" OG1 THR B 307 " model vdw 1.967 3.040 nonbonded pdb=" O SER G 297 " pdb=" OG SER G 321 " model vdw 1.996 3.040 nonbonded pdb=" OG1 THR A 277 " pdb=" OG SER A 284 " model vdw 2.016 3.040 nonbonded pdb=" OE1 GLN F 179 " pdb=" OG1 THR F 263 " model vdw 2.044 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" OG1 THR A 307 " model vdw 2.061 3.040 ... (remaining 180912 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 'A' selection = (chain 'B' and resid 1 through 344) selection = (chain 'C' and resid 1 through 344) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'V' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 23319 Z= 0.294 Angle : 0.854 11.665 31783 Z= 0.500 Chirality : 0.057 0.667 3490 Planarity : 0.010 0.276 4104 Dihedral : 12.491 89.893 8344 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 2897 helix: -2.61 (0.56), residues: 66 sheet: -0.26 (0.15), residues: 1151 loop : -0.50 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 223 TYR 0.029 0.002 TYR G 15 PHE 0.036 0.002 PHE X 67 TRP 0.020 0.002 TRP W 103 HIS 0.008 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.29 (23264) covalent geometry : angle 0.84873 / 0.50 (31663) SS BOND : bond 0.00649 / 0.51 ( 45) SS BOND : angle 1.70347 / 1.08 ( 90) hydrogen bonds : bond 0.13579 / 9.22 ( 776) hydrogen bonds : angle 7.55968 / 5.18 ( 1992) link_BETA1-4 : bond 0.00098 / 0.05 ( 4) link_BETA1-4 : angle 1.94411 / 1.05 ( 12) link_NAG-ASN : bond 0.00461 / 0.20 ( 6) link_NAG-ASN : angle 1.86920 / 1.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 663 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 47 TRP cc_start: 0.7165 (t60) cc_final: 0.6705 (t60) REVERT: X 100 TYR cc_start: 0.7693 (t80) cc_final: 0.7459 (t80) REVERT: X 100 HIS cc_start: 0.7138 (m90) cc_final: 0.6911 (m-70) REVERT: G 72 TYR cc_start: 0.6578 (m-10) cc_final: 0.6370 (m-80) REVERT: G 142 ILE cc_start: 0.7969 (pt) cc_final: 0.7689 (mt) REVERT: G 202 ASP cc_start: 0.7876 (p0) cc_final: 0.7494 (p0) REVERT: G 246 ASP cc_start: 0.6845 (m-30) cc_final: 0.6521 (m-30) REVERT: E 128 SER cc_start: 0.8456 (t) cc_final: 0.8143 (p) REVERT: E 202 ASP cc_start: 0.7858 (p0) cc_final: 0.7657 (p0) REVERT: E 304 ASN cc_start: 0.7049 (m110) cc_final: 0.6515 (m110) REVERT: E 311 ASP cc_start: 0.6734 (p0) cc_final: 0.6386 (p0) REVERT: E 319 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7968 (mmmt) REVERT: C 3 GLU cc_start: 0.7775 (tp30) cc_final: 0.7569 (tp30) REVERT: C 53 TYR cc_start: 0.8473 (m-80) cc_final: 0.7946 (m-80) REVERT: C 70 MET cc_start: 0.7890 (tpp) cc_final: 0.7563 (tpt) REVERT: C 112 MET cc_start: 0.7983 (ttm) cc_final: 0.7726 (ttt) REVERT: C 313 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6702 (mt-10) REVERT: F 29 ILE cc_start: 0.8265 (mt) cc_final: 0.8046 (mt) REVERT: F 186 ASN cc_start: 0.8514 (m-40) cc_final: 0.7923 (m-40) REVERT: F 319 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8371 (mtpp) REVERT: F 341 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7166 (mt-10) REVERT: F 353 THR cc_start: 0.8161 (p) cc_final: 0.7913 (p) REVERT: F 356 PHE cc_start: 0.7748 (p90) cc_final: 0.7546 (p90) REVERT: F 402 VAL cc_start: 0.3867 (p) cc_final: 0.2594 (m) REVERT: B 53 TYR cc_start: 0.8156 (m-80) cc_final: 0.7866 (m-80) REVERT: B 84 LEU cc_start: 0.8064 (pt) cc_final: 0.7801 (pp) REVERT: B 112 MET cc_start: 0.8419 (ttt) cc_final: 0.8109 (ttp) REVERT: B 130 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7994 (mtpp) REVERT: B 137 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6375 (mt-10) REVERT: B 148 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6931 (mm-30) REVERT: B 161 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7049 (mmt90) REVERT: B 238 TYR cc_start: 0.7526 (t80) cc_final: 0.7034 (t80) REVERT: B 275 MET cc_start: 0.7218 (mtm) cc_final: 0.7007 (mtp) REVERT: B 282 SER cc_start: 0.8338 (t) cc_final: 0.8079 (p) REVERT: B 332 ASN cc_start: 0.8461 (m-40) cc_final: 0.7778 (m110) REVERT: A 8 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 57 SER cc_start: 0.8436 (m) cc_final: 0.8080 (t) REVERT: A 88 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7914 (mtp180) REVERT: A 224 GLU cc_start: 0.7592 (tp30) cc_final: 0.7330 (tp30) REVERT: A 254 LYS cc_start: 0.7714 (mttp) cc_final: 0.6993 (mtmm) REVERT: A 276 ILE cc_start: 0.8913 (mm) cc_final: 0.8541 (mm) REVERT: W 100 TYR cc_start: 0.7989 (t80) cc_final: 0.7682 (t80) REVERT: V 54 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.6979 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.1515 time to fit residues: 155.6739 Evaluate side-chains 605 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 605 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.0370 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 196 GLN G 204 GLN G 304 ASN E 20 ASN E 118 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 270 ASN E 362 HIS E 392 GLN E 396 GLN C 141 HIS C 305 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 355 HIS F 362 HIS ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS A 132 ASN A 159 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113969 restraints weight = 36975.954| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.19 r_work: 0.3337 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23319 Z= 0.126 Angle : 0.639 7.932 31783 Z= 0.331 Chirality : 0.046 0.240 3490 Planarity : 0.005 0.053 4104 Dihedral : 5.624 57.475 3184 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.67 % Allowed : 9.77 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 2897 helix: -2.70 (0.52), residues: 66 sheet: -0.04 (0.15), residues: 1088 loop : -0.48 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 267 TYR 0.018 0.001 TYR G 122 PHE 0.023 0.002 PHE G 365 TRP 0.014 0.001 TRP X 99 HIS 0.008 0.001 HIS H 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (23264) covalent geometry : angle 0.63626 / 0.33 (31663) SS BOND : bond 0.00274 / 0.20 ( 45) SS BOND : angle 0.98927 / 0.65 ( 90) hydrogen bonds : bond 0.03500 / 2.35 ( 776) hydrogen bonds : angle 6.25100 / 4.32 ( 1992) link_BETA1-4 : bond 0.00458 / 0.24 ( 4) link_BETA1-4 : angle 1.33885 / 0.69 ( 12) link_NAG-ASN : bond 0.00380 / 0.25 ( 6) link_NAG-ASN : angle 1.38845 / 0.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 641 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6822 (tp) cc_final: 0.6393 (tp) REVERT: G 142 ILE cc_start: 0.8148 (pt) cc_final: 0.7894 (mt) REVERT: G 202 ASP cc_start: 0.8161 (p0) cc_final: 0.7843 (p0) REVERT: G 210 SER cc_start: 0.8484 (t) cc_final: 0.8261 (t) REVERT: G 220 VAL cc_start: 0.8408 (p) cc_final: 0.8043 (t) REVERT: G 222 GLN cc_start: 0.8186 (mp10) cc_final: 0.7925 (mp10) REVERT: G 246 ASP cc_start: 0.7546 (m-30) cc_final: 0.7177 (m-30) REVERT: E 94 CYS cc_start: 0.7304 (m) cc_final: 0.6762 (m) REVERT: E 114 CYS cc_start: 0.7278 (t) cc_final: 0.6773 (t) REVERT: E 222 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8527 (mp10) REVERT: E 238 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7601 (m) REVERT: E 304 ASN cc_start: 0.7560 (m110) cc_final: 0.7036 (m110) REVERT: E 327 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7377 (mmmm) REVERT: E 349 GLN cc_start: 0.7365 (pm20) cc_final: 0.7030 (pm20) REVERT: C 42 ASP cc_start: 0.7215 (p0) cc_final: 0.6753 (p0) REVERT: C 53 TYR cc_start: 0.8653 (m-80) cc_final: 0.8331 (m-80) REVERT: C 66 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7472 (ttp) REVERT: C 70 MET cc_start: 0.8023 (tpp) cc_final: 0.7750 (tpt) REVERT: C 112 MET cc_start: 0.8586 (ttm) cc_final: 0.8142 (ttt) REVERT: C 313 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7762 (mt-10) REVERT: F 38 LEU cc_start: 0.7408 (tp) cc_final: 0.7188 (tt) REVERT: F 45 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7742 (mm-30) REVERT: F 186 ASN cc_start: 0.8789 (m-40) cc_final: 0.8423 (m-40) REVERT: F 315 ILE cc_start: 0.7995 (mp) cc_final: 0.7715 (mm) REVERT: F 319 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8298 (mtpp) REVERT: F 341 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7733 (mt-10) REVERT: F 353 THR cc_start: 0.8390 (p) cc_final: 0.8186 (p) REVERT: F 402 VAL cc_start: 0.4578 (p) cc_final: 0.3018 (m) REVERT: B 49 THR cc_start: 0.8372 (m) cc_final: 0.8135 (p) REVERT: B 112 MET cc_start: 0.8783 (ttt) cc_final: 0.8471 (ttp) REVERT: B 130 LYS cc_start: 0.8442 (mtmm) cc_final: 0.8147 (mtpp) REVERT: B 148 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7422 (mm-30) REVERT: B 154 TYR cc_start: 0.8752 (m-80) cc_final: 0.8483 (m-80) REVERT: B 164 TYR cc_start: 0.8584 (m-80) cc_final: 0.8136 (m-80) REVERT: B 231 LEU cc_start: 0.8884 (tp) cc_final: 0.8642 (tt) REVERT: B 275 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: A 127 TYR cc_start: 0.8735 (m-80) cc_final: 0.8535 (m-80) REVERT: A 130 LYS cc_start: 0.8133 (pttm) cc_final: 0.7776 (pttm) REVERT: A 175 ASP cc_start: 0.7923 (t0) cc_final: 0.7450 (t0) REVERT: A 177 SER cc_start: 0.8824 (m) cc_final: 0.8271 (p) REVERT: A 254 LYS cc_start: 0.8242 (mttp) cc_final: 0.7840 (tttp) REVERT: A 276 ILE cc_start: 0.8973 (mm) cc_final: 0.8517 (mm) REVERT: H 31 ASP cc_start: 0.7651 (m-30) cc_final: 0.7392 (m-30) REVERT: H 76 ASN cc_start: 0.8413 (t0) cc_final: 0.8070 (t0) REVERT: W 59 PHE cc_start: 0.7601 (m-80) cc_final: 0.6975 (m-80) REVERT: V 2 MET cc_start: 0.4776 (tpp) cc_final: 0.4496 (tpt) outliers start: 41 outliers final: 22 residues processed: 648 average time/residue: 0.1547 time to fit residues: 155.1860 Evaluate side-chains 617 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 592 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 286 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 94 optimal weight: 0.0170 chunk 167 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 HIS G 179 GLN G 204 GLN G 392 GLN C 141 HIS C 288 HIS C 341 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN F 157 ASN F 235 GLN F 349 GLN ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 288 HIS A 132 ASN A 299 GLN A 332 ASN W 100DHIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106099 restraints weight = 37347.054| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.25 r_work: 0.3245 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 23319 Z= 0.334 Angle : 0.718 9.122 31783 Z= 0.376 Chirality : 0.048 0.228 3490 Planarity : 0.006 0.053 4104 Dihedral : 6.084 68.617 3184 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.14 % Allowed : 13.19 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.15), residues: 2897 helix: -2.63 (0.53), residues: 66 sheet: -0.07 (0.15), residues: 1114 loop : -0.70 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 50 TYR 0.025 0.003 TYR V 49 PHE 0.028 0.003 PHE F 365 TRP 0.024 0.003 TRP X 99 HIS 0.011 0.002 HIS H 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.33 (23264) covalent geometry : angle 0.71492 / 0.38 (31663) SS BOND : bond 0.00537 / 0.36 ( 45) SS BOND : angle 1.21001 / 0.79 ( 90) hydrogen bonds : bond 0.04056 / 2.76 ( 776) hydrogen bonds : angle 6.25893 / 4.35 ( 1992) link_BETA1-4 : bond 0.00531 / 0.26 ( 4) link_BETA1-4 : angle 1.73798 / 0.97 ( 12) link_NAG-ASN : bond 0.00303 / 0.15 ( 6) link_NAG-ASN : angle 1.26806 / 0.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 639 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 38 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8078 (tp) REVERT: G 76 GLU cc_start: 0.7317 (tt0) cc_final: 0.7073 (pt0) REVERT: G 202 ASP cc_start: 0.8242 (p0) cc_final: 0.7987 (p0) REVERT: G 210 SER cc_start: 0.8559 (t) cc_final: 0.8339 (t) REVERT: G 220 VAL cc_start: 0.8405 (p) cc_final: 0.8036 (t) REVERT: G 222 GLN cc_start: 0.8080 (mp10) cc_final: 0.7766 (mp10) REVERT: G 246 ASP cc_start: 0.7587 (m-30) cc_final: 0.7153 (m-30) REVERT: G 269 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7786 (mt-10) REVERT: G 309 SER cc_start: 0.7939 (t) cc_final: 0.7737 (t) REVERT: G 402 VAL cc_start: 0.4171 (OUTLIER) cc_final: 0.2519 (t) REVERT: E 1 TYR cc_start: 0.7578 (t80) cc_final: 0.7268 (t80) REVERT: E 94 CYS cc_start: 0.7639 (m) cc_final: 0.7137 (m) REVERT: E 114 CYS cc_start: 0.7504 (t) cc_final: 0.7090 (t) REVERT: E 304 ASN cc_start: 0.7644 (m110) cc_final: 0.7145 (m110) REVERT: E 311 ASP cc_start: 0.7761 (p0) cc_final: 0.7494 (p0) REVERT: E 315 ILE cc_start: 0.7972 (mm) cc_final: 0.7689 (mm) REVERT: E 319 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8182 (mmmt) REVERT: E 327 LYS cc_start: 0.7647 (mmmm) cc_final: 0.7367 (mmmm) REVERT: C 42 ASP cc_start: 0.7339 (p0) cc_final: 0.7097 (p0) REVERT: C 70 MET cc_start: 0.7838 (tpp) cc_final: 0.7596 (tpt) REVERT: C 108 ASP cc_start: 0.7724 (m-30) cc_final: 0.7426 (m-30) REVERT: C 112 MET cc_start: 0.8674 (ttm) cc_final: 0.8451 (ttm) REVERT: C 157 ASP cc_start: 0.8394 (t0) cc_final: 0.7972 (t0) REVERT: C 205 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8111 (p) REVERT: C 313 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7858 (mt-10) REVERT: C 336 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8220 (mmtp) REVERT: F 45 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7887 (mm-30) REVERT: F 99 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7871 (mp0) REVERT: F 174 ASP cc_start: 0.7507 (p0) cc_final: 0.7130 (p0) REVERT: F 186 ASN cc_start: 0.8747 (m-40) cc_final: 0.7697 (m-40) REVERT: F 260 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7077 (mt-10) REVERT: F 270 ASN cc_start: 0.8381 (m-40) cc_final: 0.7947 (m110) REVERT: F 309 SER cc_start: 0.7718 (t) cc_final: 0.7464 (p) REVERT: F 315 ILE cc_start: 0.8100 (mp) cc_final: 0.7820 (mm) REVERT: F 319 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8403 (mtpp) REVERT: F 341 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7669 (mt-10) REVERT: F 353 THR cc_start: 0.8490 (p) cc_final: 0.8252 (p) REVERT: B 28 HIS cc_start: 0.8330 (m90) cc_final: 0.7696 (m90) REVERT: B 49 THR cc_start: 0.8446 (m) cc_final: 0.8059 (p) REVERT: B 94 ASP cc_start: 0.7728 (t0) cc_final: 0.7500 (t0) REVERT: B 148 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7573 (mm-30) REVERT: B 154 TYR cc_start: 0.8732 (m-80) cc_final: 0.8399 (m-80) REVERT: B 275 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: B 276 ILE cc_start: 0.8744 (mp) cc_final: 0.8460 (mt) REVERT: A 62 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7722 (tttt) REVERT: A 149 GLN cc_start: 0.8497 (tt0) cc_final: 0.8289 (mt0) REVERT: A 276 ILE cc_start: 0.8984 (mm) cc_final: 0.8614 (mm) REVERT: H 31 ASP cc_start: 0.7660 (m-30) cc_final: 0.7396 (m-30) REVERT: H 76 ASN cc_start: 0.8450 (t0) cc_final: 0.8012 (t0) REVERT: H 91 TYR cc_start: 0.6988 (m-80) cc_final: 0.6460 (m-80) REVERT: W 59 PHE cc_start: 0.7456 (m-80) cc_final: 0.6869 (m-80) REVERT: V 89 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8502 (tm-30) outliers start: 77 outliers final: 53 residues processed: 671 average time/residue: 0.1433 time to fit residues: 151.9956 Evaluate side-chains 678 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 621 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 43 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 47 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 151 optimal weight: 0.0470 chunk 258 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 218 ASN G 270 ASN G 304 ASN ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 341 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 288 HIS A 152 GLN A 288 HIS ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108061 restraints weight = 37129.671| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.20 r_work: 0.3283 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23319 Z= 0.201 Angle : 0.641 11.025 31783 Z= 0.334 Chirality : 0.045 0.235 3490 Planarity : 0.005 0.050 4104 Dihedral : 5.801 68.855 3184 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.62 % Allowed : 15.31 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 2897 helix: -1.70 (0.68), residues: 48 sheet: -0.07 (0.15), residues: 1127 loop : -0.64 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 161 TYR 0.019 0.002 TYR F 15 PHE 0.036 0.002 PHE A 280 TRP 0.018 0.002 TRP X 99 HIS 0.011 0.001 HIS H 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (23264) covalent geometry : angle 0.63881 / 0.33 (31663) SS BOND : bond 0.00404 / 0.27 ( 45) SS BOND : angle 1.11331 / 0.78 ( 90) hydrogen bonds : bond 0.03484 / 2.39 ( 776) hydrogen bonds : angle 6.04837 / 4.20 ( 1992) link_BETA1-4 : bond 0.00306 / 0.15 ( 4) link_BETA1-4 : angle 1.36192 / 0.75 ( 12) link_NAG-ASN : bond 0.00069 / 0.03 ( 6) link_NAG-ASN : angle 0.99859 / 0.58 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 625 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6597 (tp) cc_final: 0.6244 (tp) REVERT: G 76 GLU cc_start: 0.7346 (tt0) cc_final: 0.7092 (pt0) REVERT: G 202 ASP cc_start: 0.8206 (p0) cc_final: 0.7969 (p0) REVERT: G 210 SER cc_start: 0.8569 (t) cc_final: 0.8346 (t) REVERT: G 220 VAL cc_start: 0.8321 (p) cc_final: 0.7983 (t) REVERT: G 246 ASP cc_start: 0.7578 (m-30) cc_final: 0.7138 (m-30) REVERT: G 309 SER cc_start: 0.7956 (t) cc_final: 0.7699 (t) REVERT: G 389 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8429 (t) REVERT: G 402 VAL cc_start: 0.4174 (OUTLIER) cc_final: 0.2657 (t) REVERT: E 1 TYR cc_start: 0.7477 (t80) cc_final: 0.7139 (t80) REVERT: E 94 CYS cc_start: 0.7681 (m) cc_final: 0.7220 (m) REVERT: E 304 ASN cc_start: 0.7562 (m110) cc_final: 0.7043 (m110) REVERT: E 311 ASP cc_start: 0.7658 (p0) cc_final: 0.7243 (p0) REVERT: E 315 ILE cc_start: 0.7905 (mm) cc_final: 0.7615 (mm) REVERT: E 319 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8175 (mmmt) REVERT: E 327 LYS cc_start: 0.7635 (mmmm) cc_final: 0.7345 (mmmm) REVERT: C 42 ASP cc_start: 0.7378 (p0) cc_final: 0.7085 (p0) REVERT: C 53 TYR cc_start: 0.8576 (m-80) cc_final: 0.8363 (m-80) REVERT: C 70 MET cc_start: 0.7906 (tpp) cc_final: 0.7701 (tpt) REVERT: C 108 ASP cc_start: 0.7679 (m-30) cc_final: 0.7366 (m-30) REVERT: C 112 MET cc_start: 0.8666 (ttm) cc_final: 0.8434 (ttm) REVERT: C 157 ASP cc_start: 0.8329 (t0) cc_final: 0.7925 (t0) REVERT: C 205 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8034 (p) REVERT: C 313 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7858 (mt-10) REVERT: C 337 ARG cc_start: 0.8378 (mmt90) cc_final: 0.8160 (mpt-90) REVERT: F 99 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7849 (mp0) REVERT: F 260 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7000 (mt-10) REVERT: F 270 ASN cc_start: 0.8354 (m-40) cc_final: 0.7881 (m110) REVERT: F 315 ILE cc_start: 0.8039 (mp) cc_final: 0.7757 (mm) REVERT: F 319 LYS cc_start: 0.8600 (mtpp) cc_final: 0.8386 (mtpp) REVERT: F 353 THR cc_start: 0.8468 (p) cc_final: 0.8259 (p) REVERT: F 402 VAL cc_start: 0.4169 (p) cc_final: 0.2623 (m) REVERT: B 28 HIS cc_start: 0.8283 (m90) cc_final: 0.7642 (m90) REVERT: B 49 THR cc_start: 0.8362 (m) cc_final: 0.8065 (p) REVERT: B 94 ASP cc_start: 0.7725 (t0) cc_final: 0.7511 (t0) REVERT: B 130 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8194 (mtpp) REVERT: B 148 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7516 (mm-30) REVERT: B 154 TYR cc_start: 0.8743 (m-80) cc_final: 0.8500 (m-80) REVERT: B 166 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7328 (mm-30) REVERT: B 266 CYS cc_start: 0.7582 (m) cc_final: 0.7254 (m) REVERT: B 276 ILE cc_start: 0.8711 (mp) cc_final: 0.8446 (mt) REVERT: A 21 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7399 (mtp85) REVERT: A 62 LYS cc_start: 0.8270 (ttmm) cc_final: 0.7904 (tttp) REVERT: A 65 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (p) REVERT: A 124 SER cc_start: 0.8534 (t) cc_final: 0.7920 (p) REVERT: A 175 ASP cc_start: 0.8187 (t0) cc_final: 0.7762 (t0) REVERT: A 177 SER cc_start: 0.8827 (m) cc_final: 0.8411 (p) REVERT: A 275 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7561 (mtm) REVERT: A 276 ILE cc_start: 0.8986 (mm) cc_final: 0.8759 (mm) REVERT: H 31 ASP cc_start: 0.7704 (m-30) cc_final: 0.7395 (m-30) REVERT: H 76 ASN cc_start: 0.8427 (t0) cc_final: 0.8004 (t0) REVERT: H 91 TYR cc_start: 0.6937 (m-80) cc_final: 0.6676 (m-80) REVERT: W 59 PHE cc_start: 0.7572 (m-80) cc_final: 0.7072 (m-80) outliers start: 89 outliers final: 60 residues processed: 669 average time/residue: 0.1478 time to fit residues: 155.0365 Evaluate side-chains 679 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 613 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 105 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 270 ASN ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN F 157 ASN F 349 GLN B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS A 132 ASN A 152 GLN A 159 GLN A 216 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106005 restraints weight = 37134.448| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.20 r_work: 0.3271 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 23319 Z= 0.302 Angle : 0.695 11.041 31783 Z= 0.363 Chirality : 0.047 0.214 3490 Planarity : 0.005 0.055 4104 Dihedral : 6.000 74.308 3184 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.23 % Allowed : 16.25 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 2897 helix: -1.66 (0.67), residues: 48 sheet: -0.16 (0.15), residues: 1139 loop : -0.80 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 161 TYR 0.023 0.002 TYR V 49 PHE 0.027 0.002 PHE F 365 TRP 0.023 0.002 TRP X 99 HIS 0.012 0.002 HIS H 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.30 (23264) covalent geometry : angle 0.69155 / 0.36 (31663) SS BOND : bond 0.00536 / 0.37 ( 45) SS BOND : angle 1.34475 / 0.90 ( 90) hydrogen bonds : bond 0.03816 / 2.63 ( 776) hydrogen bonds : angle 6.13459 / 4.27 ( 1992) link_BETA1-4 : bond 0.00345 / 0.17 ( 4) link_BETA1-4 : angle 1.40111 / 0.76 ( 12) link_NAG-ASN : bond 0.00266 / 0.15 ( 6) link_NAG-ASN : angle 1.27789 / 0.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 633 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 99 TRP cc_start: 0.7891 (p-90) cc_final: 0.7415 (p-90) REVERT: Y 73 LEU cc_start: 0.6679 (tp) cc_final: 0.6274 (tp) REVERT: G 76 GLU cc_start: 0.7362 (tt0) cc_final: 0.7095 (pt0) REVERT: G 117 ASP cc_start: 0.8111 (t0) cc_final: 0.7804 (t70) REVERT: G 202 ASP cc_start: 0.8197 (p0) cc_final: 0.7982 (p0) REVERT: G 220 VAL cc_start: 0.8299 (p) cc_final: 0.7986 (t) REVERT: G 241 GLU cc_start: 0.7463 (tt0) cc_final: 0.7042 (tt0) REVERT: G 246 ASP cc_start: 0.7579 (m-30) cc_final: 0.7126 (m-30) REVERT: G 264 ASN cc_start: 0.8179 (m-40) cc_final: 0.7932 (m-40) REVERT: G 309 SER cc_start: 0.7960 (t) cc_final: 0.7706 (t) REVERT: G 384 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8219 (mtpp) REVERT: G 389 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8417 (t) REVERT: G 402 VAL cc_start: 0.4296 (OUTLIER) cc_final: 0.2628 (t) REVERT: E 1 TYR cc_start: 0.7499 (t80) cc_final: 0.7282 (t80) REVERT: E 94 CYS cc_start: 0.7669 (m) cc_final: 0.7194 (m) REVERT: E 157 ASN cc_start: 0.8780 (m-40) cc_final: 0.8560 (m-40) REVERT: E 304 ASN cc_start: 0.7585 (m110) cc_final: 0.7115 (m110) REVERT: E 311 ASP cc_start: 0.7653 (p0) cc_final: 0.7234 (p0) REVERT: E 315 ILE cc_start: 0.7948 (mm) cc_final: 0.7671 (mm) REVERT: E 319 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8142 (mmmt) REVERT: E 327 LYS cc_start: 0.7663 (mmmm) cc_final: 0.7368 (mmmm) REVERT: C 42 ASP cc_start: 0.7374 (p0) cc_final: 0.7136 (p0) REVERT: C 112 MET cc_start: 0.8681 (ttm) cc_final: 0.8451 (ttm) REVERT: C 157 ASP cc_start: 0.8282 (t0) cc_final: 0.7933 (t0) REVERT: C 186 VAL cc_start: 0.7732 (t) cc_final: 0.7447 (p) REVERT: C 205 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 313 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7842 (mt-10) REVERT: F 98 THR cc_start: 0.7076 (t) cc_final: 0.6861 (t) REVERT: F 99 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7717 (mp0) REVERT: F 120 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8058 (mt-10) REVERT: F 143 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7305 (t) REVERT: F 315 ILE cc_start: 0.8096 (mp) cc_final: 0.7799 (mm) REVERT: F 319 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8412 (mtpp) REVERT: B 28 HIS cc_start: 0.8308 (m90) cc_final: 0.7643 (m90) REVERT: B 49 THR cc_start: 0.8347 (m) cc_final: 0.8045 (p) REVERT: B 66 MET cc_start: 0.8296 (ttm) cc_final: 0.8060 (ttm) REVERT: B 94 ASP cc_start: 0.7841 (t0) cc_final: 0.7638 (t0) REVERT: B 130 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8194 (mtpp) REVERT: B 148 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 166 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7339 (mm-30) REVERT: B 182 SER cc_start: 0.7936 (t) cc_final: 0.7637 (m) REVERT: B 275 MET cc_start: 0.8404 (mtm) cc_final: 0.8168 (mtp) REVERT: B 276 ILE cc_start: 0.8766 (mp) cc_final: 0.8474 (mt) REVERT: A 21 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7429 (mtp85) REVERT: A 31 ILE cc_start: 0.8419 (tp) cc_final: 0.8023 (tp) REVERT: A 62 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7834 (mttt) REVERT: A 65 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 124 SER cc_start: 0.8524 (t) cc_final: 0.7892 (p) REVERT: A 175 ASP cc_start: 0.8058 (t0) cc_final: 0.7606 (t0) REVERT: A 177 SER cc_start: 0.8856 (m) cc_final: 0.8312 (p) REVERT: A 224 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: A 273 GLU cc_start: 0.8396 (pt0) cc_final: 0.8172 (pt0) REVERT: A 275 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7554 (mtm) REVERT: A 276 ILE cc_start: 0.8988 (mm) cc_final: 0.8773 (mm) REVERT: H 31 ASP cc_start: 0.7705 (m-30) cc_final: 0.7438 (m-30) REVERT: W 59 PHE cc_start: 0.7491 (m-80) cc_final: 0.6832 (m-80) REVERT: V 2 MET cc_start: 0.3709 (tpt) cc_final: 0.3292 (tpt) REVERT: V 54 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7760 (mtt180) outliers start: 104 outliers final: 75 residues processed: 686 average time/residue: 0.1503 time to fit residues: 162.3243 Evaluate side-chains 700 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 617 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 63 CYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 ASP Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 341 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 218 optimal weight: 0.9980 chunk 217 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 chunk 282 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 270 ASN ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN C 141 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN F 355 HIS B 132 ASN A 152 GLN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108856 restraints weight = 37690.981| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.28 r_work: 0.3302 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23319 Z= 0.137 Angle : 0.621 11.161 31783 Z= 0.321 Chirality : 0.045 0.208 3490 Planarity : 0.005 0.051 4104 Dihedral : 5.565 69.588 3184 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.54 % Allowed : 18.36 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 2897 helix: -1.49 (0.70), residues: 48 sheet: -0.01 (0.15), residues: 1124 loop : -0.66 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 52 TYR 0.018 0.001 TYR F 15 PHE 0.027 0.002 PHE F 365 TRP 0.023 0.001 TRP L 35 HIS 0.010 0.001 HIS H 52A Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (23264) covalent geometry : angle 0.61911 / 0.32 (31663) SS BOND : bond 0.00311 / 0.22 ( 45) SS BOND : angle 1.05922 / 0.67 ( 90) hydrogen bonds : bond 0.03175 / 2.19 ( 776) hydrogen bonds : angle 5.88793 / 4.09 ( 1992) link_BETA1-4 : bond 0.00393 / 0.19 ( 4) link_BETA1-4 : angle 1.26674 / 0.69 ( 12) link_NAG-ASN : bond 0.00126 / 0.05 ( 6) link_NAG-ASN : angle 0.81964 / 0.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 637 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 99 TRP cc_start: 0.7832 (p-90) cc_final: 0.7388 (p-90) REVERT: Y 73 LEU cc_start: 0.6615 (tp) cc_final: 0.6196 (tp) REVERT: G 76 GLU cc_start: 0.7473 (tt0) cc_final: 0.7162 (pt0) REVERT: G 202 ASP cc_start: 0.8180 (p0) cc_final: 0.7960 (p0) REVERT: G 220 VAL cc_start: 0.8290 (p) cc_final: 0.7976 (t) REVERT: G 246 ASP cc_start: 0.7550 (m-30) cc_final: 0.7111 (m-30) REVERT: G 309 SER cc_start: 0.7917 (t) cc_final: 0.7643 (t) REVERT: G 402 VAL cc_start: 0.4007 (OUTLIER) cc_final: 0.2460 (t) REVERT: E 15 TYR cc_start: 0.8614 (t80) cc_final: 0.8368 (t80) REVERT: E 94 CYS cc_start: 0.7604 (m) cc_final: 0.7167 (m) REVERT: E 238 SER cc_start: 0.7826 (OUTLIER) cc_final: 0.7623 (t) REVERT: E 304 ASN cc_start: 0.7497 (m110) cc_final: 0.7011 (m110) REVERT: E 315 ILE cc_start: 0.7898 (mm) cc_final: 0.7613 (mm) REVERT: E 319 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8157 (mmmt) REVERT: E 327 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7377 (mmmm) REVERT: C 42 ASP cc_start: 0.7310 (p0) cc_final: 0.7072 (p0) REVERT: C 81 GLN cc_start: 0.8764 (mm110) cc_final: 0.8115 (mt0) REVERT: C 157 ASP cc_start: 0.8273 (t0) cc_final: 0.7976 (t0) REVERT: C 205 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 313 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7914 (mt-10) REVERT: F 315 ILE cc_start: 0.8130 (mp) cc_final: 0.7814 (mm) REVERT: F 319 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8359 (mtpp) REVERT: F 346 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8304 (tp) REVERT: F 402 VAL cc_start: 0.4506 (p) cc_final: 0.2996 (m) REVERT: B 28 HIS cc_start: 0.8150 (m90) cc_final: 0.7655 (m90) REVERT: B 66 MET cc_start: 0.8276 (ttm) cc_final: 0.7947 (ttm) REVERT: B 148 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 166 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 182 SER cc_start: 0.7930 (t) cc_final: 0.7689 (m) REVERT: B 197 LEU cc_start: 0.8759 (tt) cc_final: 0.8452 (tp) REVERT: B 216 GLN cc_start: 0.7415 (tt0) cc_final: 0.7102 (tt0) REVERT: B 276 ILE cc_start: 0.8727 (mp) cc_final: 0.8444 (mt) REVERT: A 21 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7366 (mtp85) REVERT: A 31 ILE cc_start: 0.8397 (tp) cc_final: 0.8018 (tp) REVERT: A 62 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7979 (tttp) REVERT: A 124 SER cc_start: 0.8467 (t) cc_final: 0.7900 (p) REVERT: A 159 GLN cc_start: 0.8494 (pt0) cc_final: 0.8027 (pt0) REVERT: A 175 ASP cc_start: 0.7874 (t0) cc_final: 0.7364 (t0) REVERT: A 177 SER cc_start: 0.8852 (m) cc_final: 0.8276 (p) REVERT: A 273 GLU cc_start: 0.8305 (pt0) cc_final: 0.8054 (pt0) REVERT: A 275 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7419 (mtm) REVERT: A 276 ILE cc_start: 0.9017 (mm) cc_final: 0.8803 (mm) REVERT: H 31 ASP cc_start: 0.7754 (m-30) cc_final: 0.7513 (m-30) REVERT: H 76 ASN cc_start: 0.8451 (t0) cc_final: 0.8045 (t0) REVERT: W 59 PHE cc_start: 0.7424 (m-80) cc_final: 0.6917 (m-80) outliers start: 87 outliers final: 54 residues processed: 683 average time/residue: 0.1522 time to fit residues: 163.1341 Evaluate side-chains 681 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 621 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4365 > 50: distance: 9 - 197: 36.567 distance: 12 - 194: 32.538 distance: 22 - 182: 30.854 distance: 25 - 179: 26.589 distance: 73 - 205: 37.477 distance: 76 - 202: 27.342 distance: 128 - 156: 28.834 distance: 139 - 143: 32.268 distance: 143 - 144: 33.823 distance: 144 - 145: 8.027 distance: 144 - 147: 40.985 distance: 145 - 146: 9.512 distance: 145 - 151: 57.694 distance: 147 - 148: 38.784 distance: 148 - 149: 21.439 distance: 148 - 150: 14.997 distance: 152 - 153: 40.055 distance: 152 - 155: 38.877 distance: 153 - 154: 44.727 distance: 153 - 157: 30.305 distance: 155 - 156: 55.896 distance: 157 - 158: 39.160 distance: 158 - 161: 40.699 distance: 159 - 160: 4.983 distance: 159 - 162: 43.345 distance: 162 - 163: 21.915 distance: 163 - 164: 62.002 distance: 163 - 166: 20.860 distance: 164 - 165: 53.700 distance: 164 - 169: 27.151 distance: 166 - 167: 39.690 distance: 166 - 168: 46.023 distance: 169 - 170: 12.630 distance: 170 - 171: 42.613 distance: 171 - 172: 43.999 distance: 171 - 173: 39.622 distance: 174 - 175: 54.721 distance: 175 - 176: 48.736 distance: 175 - 179: 26.654 distance: 177 - 178: 46.756 distance: 179 - 180: 10.667 distance: 180 - 181: 42.970 distance: 180 - 183: 32.807 distance: 181 - 182: 18.365 distance: 181 - 187: 39.183 distance: 183 - 184: 47.786 distance: 183 - 185: 50.091 distance: 184 - 186: 38.837 distance: 187 - 188: 44.539 distance: 187 - 193: 8.165 distance: 188 - 189: 15.718 distance: 188 - 191: 16.179 distance: 189 - 190: 10.172 distance: 189 - 194: 45.560 distance: 191 - 192: 39.240 distance: 194 - 195: 27.562 distance: 195 - 196: 23.837 distance: 195 - 198: 43.660 distance: 196 - 197: 51.576 distance: 196 - 202: 36.317 distance: 198 - 199: 45.954 distance: 199 - 200: 57.601 distance: 199 - 201: 57.086 distance: 202 - 203: 18.436 distance: 203 - 204: 29.298 distance: 203 - 206: 56.503 distance: 204 - 205: 32.248 distance: 204 - 207: 26.376