Starting phenix.real_space_refine on Thu Jun 19 16:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8der_27396/06_2025/8der_27396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8der_27396/06_2025/8der_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8der_27396/06_2025/8der_27396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8der_27396/06_2025/8der_27396.map" model { file = "/net/cci-nas-00/data/ceres_data/8der_27396/06_2025/8der_27396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8der_27396/06_2025/8der_27396.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.59, per 1000 atoms: 0.64 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: 6.40 Conformation dependent library (CDL) restraints added in 3.1 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: 4.53 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: 8.98 Time building geometry restraints manager: 7.57 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 - 21.21: 13270 21.21 - 42.42: 675 42.42 - 63.63: 91 63.63 - 84.84: 31 84.84 - 106.04: 6 Dihedral angle restraints: 14073 sinusoidal: 5640 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 14070 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: 1.680 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: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 57.570 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 12.829 106.045 8552 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP W 103 HIS 0.008 0.001 HIS C 141 PHE 0.036 0.002 PHE X 67 TYR 0.029 0.002 TYR G 15 ARG 0.016 0.001 ARG F 223 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 6) link_NAG-ASN : angle 1.86920 ( 18) link_BETA1-4 : bond 0.00098 ( 4) link_BETA1-4 : angle 1.94411 ( 12) hydrogen bonds : bond 0.13579 ( 776) hydrogen bonds : angle 7.55968 ( 1992) SS BOND : bond 0.00649 ( 45) SS BOND : angle 1.70347 ( 90) covalent geometry : bond 0.00527 (23264) covalent geometry : angle 0.84873 (31663) *********************** 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 : 2.367 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: 0.7050 (m110) cc_final: 0.6516 (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: 0.7945 (m-80) REVERT: C 70 MET cc_start: 0.7890 (tpp) cc_final: 0.7563 (tpt) REVERT: C 112 MET cc_start: 0.7984 (ttm) cc_final: 0.7726 (ttt) REVERT: C 313 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6703 (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: 0.3493 time to fit residues: 355.8677 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 : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 261 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 16 ASN 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 W 100DHIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113156 restraints weight = 36920.018| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.19 r_work: 0.3327 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23319 Z= 0.139 Angle : 0.642 7.562 31783 Z= 0.333 Chirality : 0.046 0.240 3490 Planarity : 0.005 0.053 4104 Dihedral : 6.810 65.928 3392 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.63 % Allowed : 9.89 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2897 helix: -2.68 (0.52), residues: 66 sheet: -0.06 (0.15), residues: 1088 loop : -0.49 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 99 HIS 0.008 0.001 HIS H 52A PHE 0.023 0.002 PHE G 365 TYR 0.018 0.001 TYR G 122 ARG 0.005 0.000 ARG F 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 6) link_NAG-ASN : angle 1.35663 ( 18) link_BETA1-4 : bond 0.00492 ( 4) link_BETA1-4 : angle 1.73421 ( 12) hydrogen bonds : bond 0.03679 ( 776) hydrogen bonds : angle 6.28791 ( 1992) SS BOND : bond 0.00347 ( 45) SS BOND : angle 1.01315 ( 90) covalent geometry : bond 0.00308 (23264) covalent geometry : angle 0.63880 (31663) *********************** 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 677 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 637 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 47 TRP cc_start: 0.7257 (t60) cc_final: 0.6550 (t60) REVERT: Y 73 LEU cc_start: 0.6864 (tp) cc_final: 0.6431 (tp) REVERT: G 142 ILE cc_start: 0.8154 (pt) cc_final: 0.7904 (mt) REVERT: G 202 ASP cc_start: 0.8171 (p0) cc_final: 0.7852 (p0) REVERT: G 210 SER cc_start: 0.8487 (t) cc_final: 0.8257 (t) REVERT: G 220 VAL cc_start: 0.8438 (p) cc_final: 0.7866 (t) REVERT: G 246 ASP cc_start: 0.7537 (m-30) cc_final: 0.7164 (m-30) REVERT: E 94 CYS cc_start: 0.7327 (m) cc_final: 0.6773 (m) REVERT: E 222 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8531 (mp10) REVERT: E 304 ASN cc_start: 0.7571 (m110) cc_final: 0.7053 (m110) REVERT: E 311 ASP cc_start: 0.7515 (p0) cc_final: 0.7131 (p0) REVERT: E 327 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7382 (mmmm) REVERT: E 349 GLN cc_start: 0.7387 (pm20) cc_final: 0.7029 (pm20) REVERT: C 42 ASP cc_start: 0.7302 (p0) cc_final: 0.6840 (p0) REVERT: C 53 TYR cc_start: 0.8660 (m-80) cc_final: 0.8389 (m-80) REVERT: C 70 MET cc_start: 0.8031 (tpp) cc_final: 0.7748 (tpt) REVERT: C 112 MET cc_start: 0.8601 (ttm) cc_final: 0.8148 (ttt) REVERT: C 313 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7795 (mt-10) REVERT: F 38 LEU cc_start: 0.7453 (tp) cc_final: 0.7216 (tt) REVERT: F 45 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7803 (mm-30) REVERT: F 186 ASN cc_start: 0.8785 (m-40) cc_final: 0.8423 (m-40) REVERT: F 315 ILE cc_start: 0.8033 (mp) cc_final: 0.7760 (mm) REVERT: F 319 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8325 (mtpp) REVERT: F 341 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7728 (mt-10) REVERT: F 353 THR cc_start: 0.8408 (p) cc_final: 0.8201 (p) REVERT: F 402 VAL cc_start: 0.4545 (p) cc_final: 0.2930 (m) REVERT: B 49 THR cc_start: 0.8397 (m) cc_final: 0.8140 (p) REVERT: B 112 MET cc_start: 0.8781 (ttt) cc_final: 0.8494 (ttp) REVERT: B 130 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8182 (mtpp) REVERT: B 148 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7448 (mm-30) REVERT: B 154 TYR cc_start: 0.8753 (m-80) cc_final: 0.8478 (m-80) REVERT: B 231 LEU cc_start: 0.8884 (tp) cc_final: 0.8627 (tt) REVERT: B 275 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: A 175 ASP cc_start: 0.7966 (t0) cc_final: 0.7545 (t0) REVERT: A 177 SER cc_start: 0.8784 (m) cc_final: 0.8239 (p) REVERT: A 254 LYS cc_start: 0.8255 (mttp) cc_final: 0.7838 (tttp) REVERT: A 276 ILE cc_start: 0.8980 (mm) cc_final: 0.8534 (mm) REVERT: H 31 ASP cc_start: 0.7644 (m-30) cc_final: 0.7389 (m-30) REVERT: H 76 ASN cc_start: 0.8441 (t0) cc_final: 0.8082 (t0) REVERT: W 59 PHE cc_start: 0.7611 (m-80) cc_final: 0.6978 (m-80) REVERT: W 82 MET cc_start: 0.6523 (mtp) cc_final: 0.6235 (mtp) REVERT: W 100 TYR cc_start: 0.8134 (t80) cc_final: 0.7905 (t80) REVERT: V 2 MET cc_start: 0.4793 (tpp) cc_final: 0.4402 (tpt) REVERT: V 54 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7436 (mtt-85) outliers start: 40 outliers final: 22 residues processed: 646 average time/residue: 0.3719 time to fit residues: 373.5636 Evaluate side-chains 616 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 593 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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 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 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 129 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 110 optimal weight: 2.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 204 GLN E 392 GLN C 141 HIS C 288 HIS ** 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 288 HIS A 299 GLN A 332 ASN W 100DHIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.124774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109379 restraints weight = 36852.201| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.21 r_work: 0.3303 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23319 Z= 0.186 Angle : 0.626 9.799 31783 Z= 0.325 Chirality : 0.045 0.217 3490 Planarity : 0.005 0.050 4104 Dihedral : 6.237 61.749 3392 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.57 % Allowed : 12.50 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2897 helix: -2.58 (0.54), residues: 66 sheet: 0.03 (0.15), residues: 1085 loop : -0.54 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 99 HIS 0.008 0.001 HIS H 52A PHE 0.029 0.002 PHE F 365 TYR 0.017 0.002 TYR V 49 ARG 0.007 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 6) link_NAG-ASN : angle 0.89982 ( 18) link_BETA1-4 : bond 0.00333 ( 4) link_BETA1-4 : angle 1.57295 ( 12) hydrogen bonds : bond 0.03519 ( 776) hydrogen bonds : angle 6.05700 ( 1992) SS BOND : bond 0.00477 ( 45) SS BOND : angle 1.03864 ( 90) covalent geometry : bond 0.00411 (23264) covalent geometry : angle 0.62333 (31663) *********************** 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 672 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 609 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6844 (tp) cc_final: 0.6377 (tp) REVERT: G 142 ILE cc_start: 0.8112 (pt) cc_final: 0.7861 (mt) REVERT: G 202 ASP cc_start: 0.8189 (p0) cc_final: 0.7906 (p0) REVERT: G 210 SER cc_start: 0.8534 (t) cc_final: 0.8313 (t) REVERT: G 220 VAL cc_start: 0.8316 (p) cc_final: 0.8060 (t) REVERT: G 222 GLN cc_start: 0.8199 (mp10) cc_final: 0.7933 (mp10) REVERT: G 246 ASP cc_start: 0.7556 (m-30) cc_final: 0.7149 (m-30) REVERT: G 269 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7727 (mt-10) REVERT: G 402 VAL cc_start: 0.3781 (OUTLIER) cc_final: 0.2217 (t) REVERT: E 94 CYS cc_start: 0.7400 (m) cc_final: 0.6867 (m) REVERT: E 238 SER cc_start: 0.7919 (p) cc_final: 0.7688 (m) REVERT: E 304 ASN cc_start: 0.7607 (m110) cc_final: 0.7077 (m110) REVERT: E 311 ASP cc_start: 0.7535 (p0) cc_final: 0.7209 (p0) REVERT: E 319 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8190 (mmmt) REVERT: E 327 LYS cc_start: 0.7620 (mmmm) cc_final: 0.7350 (mmmm) REVERT: C 42 ASP cc_start: 0.7349 (p0) cc_final: 0.6969 (p0) REVERT: C 70 MET cc_start: 0.7906 (tpp) cc_final: 0.7668 (tpt) REVERT: C 157 ASP cc_start: 0.8360 (t0) cc_final: 0.7971 (t0) REVERT: C 205 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8019 (p) REVERT: C 313 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7846 (mt-10) REVERT: F 45 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7713 (mm-30) REVERT: F 99 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7852 (mp0) REVERT: F 157 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7511 (t0) REVERT: F 315 ILE cc_start: 0.8014 (mp) cc_final: 0.7750 (mm) REVERT: F 319 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8354 (mtpp) REVERT: F 402 VAL cc_start: 0.4612 (p) cc_final: 0.2974 (m) REVERT: B 28 HIS cc_start: 0.8272 (m90) cc_final: 0.7731 (m90) REVERT: B 49 THR cc_start: 0.8394 (m) cc_final: 0.8058 (p) REVERT: B 112 MET cc_start: 0.8771 (ttt) cc_final: 0.8546 (ttp) REVERT: B 148 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 154 TYR cc_start: 0.8748 (m-80) cc_final: 0.8520 (m-80) REVERT: B 161 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7610 (mpt180) REVERT: B 231 LEU cc_start: 0.8870 (tp) cc_final: 0.8636 (tt) REVERT: B 275 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: B 276 ILE cc_start: 0.8705 (mp) cc_final: 0.8420 (mt) REVERT: A 62 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7716 (tttt) REVERT: A 124 SER cc_start: 0.8453 (t) cc_final: 0.7766 (p) REVERT: A 276 ILE cc_start: 0.9008 (mm) cc_final: 0.8585 (mm) REVERT: H 31 ASP cc_start: 0.7675 (m-30) cc_final: 0.7377 (m-30) REVERT: H 67 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: H 76 ASN cc_start: 0.8393 (t0) cc_final: 0.8043 (t0) REVERT: H 82 MET cc_start: 0.6540 (mmm) cc_final: 0.6209 (mmm) REVERT: W 59 PHE cc_start: 0.7577 (m-80) cc_final: 0.6963 (m-80) REVERT: W 82 MET cc_start: 0.6286 (mtp) cc_final: 0.5986 (mtp) outliers start: 63 outliers final: 45 residues processed: 635 average time/residue: 0.3357 time to fit residues: 330.0155 Evaluate side-chains 643 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 593 time to evaluate : 2.591 ------------------------------------------------------------------------------- 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 154 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 347 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 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 171 THR 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 187 THR 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 39 ILE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 263 THR 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 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 128 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 290 LYS 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 67 PHE 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 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 199 optimal weight: 0.0770 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 129 optimal weight: 0.1980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 304 ASN G 392 GLN G 396 GLN E 355 HIS E 392 GLN C 141 HIS C 232 GLN C 341 GLN ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 288 HIS A 132 ASN A 332 ASN W 100DHIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112188 restraints weight = 37341.165| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.18 r_work: 0.3323 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23319 Z= 0.134 Angle : 0.598 11.030 31783 Z= 0.309 Chirality : 0.044 0.234 3490 Planarity : 0.005 0.049 4104 Dihedral : 5.804 61.628 3392 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.01 % Allowed : 14.90 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2897 helix: -2.49 (0.55), residues: 66 sheet: 0.11 (0.15), residues: 1083 loop : -0.48 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 99 HIS 0.010 0.001 HIS H 52A PHE 0.029 0.002 PHE F 365 TYR 0.016 0.001 TYR A 53 ARG 0.005 0.000 ARG C 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 6) link_NAG-ASN : angle 0.86508 ( 18) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 1.55122 ( 12) hydrogen bonds : bond 0.03172 ( 776) hydrogen bonds : angle 5.87963 ( 1992) SS BOND : bond 0.00322 ( 45) SS BOND : angle 0.93716 ( 90) covalent geometry : bond 0.00299 (23264) covalent geometry : angle 0.59627 (31663) *********************** 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 697 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 623 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6831 (tp) cc_final: 0.6559 (tp) REVERT: G 88 MET cc_start: 0.7732 (mtm) cc_final: 0.7521 (mtp) REVERT: G 142 ILE cc_start: 0.8101 (pt) cc_final: 0.7887 (mt) REVERT: G 202 ASP cc_start: 0.8164 (p0) cc_final: 0.7907 (p0) REVERT: G 210 SER cc_start: 0.8527 (t) cc_final: 0.8317 (t) REVERT: G 220 VAL cc_start: 0.8317 (p) cc_final: 0.7752 (t) REVERT: G 222 GLN cc_start: 0.8200 (mp10) cc_final: 0.7820 (mp10) REVERT: G 246 ASP cc_start: 0.7558 (m-30) cc_final: 0.7145 (m-30) REVERT: G 269 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7717 (mt-10) REVERT: G 389 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8453 (t) REVERT: G 402 VAL cc_start: 0.3780 (OUTLIER) cc_final: 0.2199 (t) REVERT: E 5 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7720 (p) REVERT: E 94 CYS cc_start: 0.7601 (m) cc_final: 0.7100 (m) REVERT: E 157 ASN cc_start: 0.8653 (m-40) cc_final: 0.8432 (m-40) REVERT: E 304 ASN cc_start: 0.7546 (m110) cc_final: 0.7035 (m110) REVERT: E 319 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8167 (mmmt) REVERT: E 327 LYS cc_start: 0.7618 (mmmm) cc_final: 0.7356 (mmmm) REVERT: E 349 GLN cc_start: 0.7351 (pm20) cc_final: 0.7084 (pm20) REVERT: C 42 ASP cc_start: 0.7284 (p0) cc_final: 0.6889 (p0) REVERT: C 70 MET cc_start: 0.7933 (tpp) cc_final: 0.7698 (tpt) REVERT: C 108 ASP cc_start: 0.7487 (m-30) cc_final: 0.7187 (m-30) REVERT: C 157 ASP cc_start: 0.8292 (t0) cc_final: 0.7999 (t0) REVERT: C 205 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7928 (p) REVERT: C 313 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7838 (mt-10) REVERT: F 45 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7649 (mm-30) REVERT: F 99 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7870 (mp0) REVERT: F 308 TYR cc_start: 0.7302 (t80) cc_final: 0.6921 (t80) REVERT: F 315 ILE cc_start: 0.7996 (mp) cc_final: 0.7725 (mm) REVERT: F 346 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8179 (mm) REVERT: F 402 VAL cc_start: 0.4569 (p) cc_final: 0.2915 (m) REVERT: B 28 HIS cc_start: 0.8276 (m90) cc_final: 0.7758 (m90) REVERT: B 49 THR cc_start: 0.8340 (m) cc_final: 0.8135 (p) REVERT: B 66 MET cc_start: 0.8018 (ttm) cc_final: 0.7708 (ttm) REVERT: B 130 LYS cc_start: 0.8529 (mtmm) cc_final: 0.8168 (mtpp) REVERT: B 148 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7488 (mm-30) REVERT: B 166 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7278 (mm-30) REVERT: B 231 LEU cc_start: 0.8867 (tp) cc_final: 0.8638 (tt) REVERT: B 275 MET cc_start: 0.8436 (mtm) cc_final: 0.8168 (mtp) REVERT: B 276 ILE cc_start: 0.8723 (mp) cc_final: 0.8469 (mt) REVERT: B 286 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8116 (mtpt) REVERT: A 62 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7843 (tttt) REVERT: A 124 SER cc_start: 0.8389 (t) cc_final: 0.7813 (p) REVERT: A 175 ASP cc_start: 0.8075 (t0) cc_final: 0.7753 (t0) REVERT: A 177 SER cc_start: 0.8818 (m) cc_final: 0.8448 (p) REVERT: A 275 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7648 (mtm) REVERT: A 276 ILE cc_start: 0.8984 (mm) cc_final: 0.8603 (mm) REVERT: H 31 ASP cc_start: 0.7708 (m-30) cc_final: 0.7448 (m-30) REVERT: H 76 ASN cc_start: 0.8388 (t0) cc_final: 0.8029 (t0) REVERT: W 59 PHE cc_start: 0.7571 (m-80) cc_final: 0.7053 (m-80) outliers start: 74 outliers final: 50 residues processed: 655 average time/residue: 0.3336 time to fit residues: 339.7334 Evaluate side-chains 664 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 608 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 THR Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR 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 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 187 THR 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 266 CYS 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 103 VAL Chi-restraints excluded: chain F residue 143 VAL 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 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 65 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 LYS 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 5 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 190 optimal weight: 0.0020 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 34 HIS ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 HIS G 392 GLN G 396 GLN E 270 ASN C 141 HIS C 232 GLN F 10 GLN F 77 GLN F 349 GLN ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107398 restraints weight = 37456.421| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.27 r_work: 0.3278 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23319 Z= 0.228 Angle : 0.640 10.960 31783 Z= 0.333 Chirality : 0.046 0.217 3490 Planarity : 0.005 0.048 4104 Dihedral : 5.874 67.380 3392 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.87 % Allowed : 14.94 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 2897 helix: -2.45 (0.55), residues: 66 sheet: 0.09 (0.15), residues: 1116 loop : -0.57 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 99 HIS 0.011 0.001 HIS H 52A PHE 0.027 0.002 PHE F 365 TYR 0.022 0.002 TYR A 53 ARG 0.005 0.000 ARG C 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 6) link_NAG-ASN : angle 0.93159 ( 18) link_BETA1-4 : bond 0.00336 ( 4) link_BETA1-4 : angle 1.58774 ( 12) hydrogen bonds : bond 0.03474 ( 776) hydrogen bonds : angle 5.89013 ( 1992) SS BOND : bond 0.00444 ( 45) SS BOND : angle 1.10652 ( 90) covalent geometry : bond 0.00504 (23264) covalent geometry : angle 0.63754 (31663) *********************** 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 723 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 628 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.7370 (tt0) cc_final: 0.7087 (pt0) REVERT: G 88 MET cc_start: 0.7870 (mtm) cc_final: 0.7649 (mtp) REVERT: G 142 ILE cc_start: 0.8027 (pt) cc_final: 0.7796 (mt) REVERT: G 202 ASP cc_start: 0.8200 (p0) cc_final: 0.7956 (p0) REVERT: G 210 SER cc_start: 0.8540 (t) cc_final: 0.8319 (t) REVERT: G 220 VAL cc_start: 0.8232 (p) cc_final: 0.8005 (t) REVERT: G 222 GLN cc_start: 0.8116 (mp10) cc_final: 0.7844 (mp10) REVERT: G 246 ASP cc_start: 0.7601 (m-30) cc_final: 0.7191 (m-30) REVERT: G 269 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7719 (mt-10) REVERT: G 358 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8791 (m) REVERT: G 389 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (t) REVERT: G 402 VAL cc_start: 0.4142 (OUTLIER) cc_final: 0.2602 (t) REVERT: E 15 TYR cc_start: 0.8544 (t80) cc_final: 0.8300 (t80) REVERT: E 94 CYS cc_start: 0.7681 (m) cc_final: 0.7205 (m) REVERT: E 304 ASN cc_start: 0.7572 (m110) cc_final: 0.7099 (m110) REVERT: E 311 ASP cc_start: 0.7750 (p0) cc_final: 0.7476 (p0) REVERT: E 319 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8165 (mmmt) REVERT: E 327 LYS cc_start: 0.7627 (mmmm) cc_final: 0.7356 (mmmm) REVERT: C 42 ASP cc_start: 0.7379 (p0) cc_final: 0.7122 (p0) REVERT: C 108 ASP cc_start: 0.7664 (m-30) cc_final: 0.7343 (m-30) REVERT: C 112 MET cc_start: 0.8570 (ttm) cc_final: 0.8204 (ttp) REVERT: C 157 ASP cc_start: 0.8305 (t0) cc_final: 0.8038 (t0) REVERT: C 205 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 313 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7851 (mt-10) REVERT: F 37 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8110 (mtmt) REVERT: F 45 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7887 (mm-30) REVERT: F 75 ASP cc_start: 0.8274 (t0) cc_final: 0.8038 (t70) REVERT: F 99 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7856 (mp0) REVERT: F 260 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6963 (mt-10) REVERT: F 308 TYR cc_start: 0.7315 (t80) cc_final: 0.7074 (t80) REVERT: F 315 ILE cc_start: 0.8063 (mp) cc_final: 0.7772 (mm) REVERT: F 402 VAL cc_start: 0.4098 (p) cc_final: 0.2527 (m) REVERT: B 28 HIS cc_start: 0.8303 (m90) cc_final: 0.7650 (m90) REVERT: B 49 THR cc_start: 0.8338 (m) cc_final: 0.8059 (p) REVERT: B 130 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8175 (mtpp) REVERT: B 148 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 166 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 231 LEU cc_start: 0.8867 (tp) cc_final: 0.8622 (tt) REVERT: B 266 CYS cc_start: 0.7598 (m) cc_final: 0.7294 (m) REVERT: B 276 ILE cc_start: 0.8701 (mp) cc_final: 0.8445 (mt) REVERT: A 21 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7366 (mtp85) REVERT: A 53 TYR cc_start: 0.8327 (m-80) cc_final: 0.8010 (m-10) REVERT: A 62 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7858 (tttp) REVERT: A 124 SER cc_start: 0.8501 (t) cc_final: 0.7861 (p) REVERT: A 175 ASP cc_start: 0.8115 (t0) cc_final: 0.7655 (t0) REVERT: A 177 SER cc_start: 0.8844 (m) cc_final: 0.8299 (p) REVERT: A 192 ASP cc_start: 0.6721 (t0) cc_final: 0.6502 (m-30) REVERT: A 224 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: A 275 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7591 (mtm) REVERT: H 31 ASP cc_start: 0.7694 (m-30) cc_final: 0.7451 (m-30) REVERT: H 76 ASN cc_start: 0.8456 (t0) cc_final: 0.8049 (t0) REVERT: W 59 PHE cc_start: 0.7550 (m-80) cc_final: 0.7057 (m-80) outliers start: 95 outliers final: 64 residues processed: 674 average time/residue: 0.3382 time to fit residues: 356.8377 Evaluate side-chains 686 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 615 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 358 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 42 VAL 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 96 CYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR 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 C residue 329 VAL 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 103 VAL Chi-restraints excluded: chain F residue 143 VAL 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 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 F residue 353 THR 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 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 65 THR Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 LYS 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 67 PHE 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 202 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 139 optimal weight: 0.0570 chunk 270 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 157 ASN G 396 GLN E 270 ASN C 141 HIS ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109787 restraints weight = 37298.180| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.23 r_work: 0.3304 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23319 Z= 0.181 Angle : 0.626 10.939 31783 Z= 0.324 Chirality : 0.045 0.222 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.713 67.103 3392 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.62 % Allowed : 16.45 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2897 helix: -2.42 (0.56), residues: 66 sheet: 0.13 (0.15), residues: 1127 loop : -0.57 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 35 HIS 0.011 0.001 HIS H 52A PHE 0.027 0.002 PHE F 365 TYR 0.024 0.002 TYR G 320 ARG 0.009 0.000 ARG A 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 6) link_NAG-ASN : angle 0.76671 ( 18) link_BETA1-4 : bond 0.00273 ( 4) link_BETA1-4 : angle 1.47593 ( 12) hydrogen bonds : bond 0.03293 ( 776) hydrogen bonds : angle 5.85932 ( 1992) SS BOND : bond 0.00387 ( 45) SS BOND : angle 1.17401 ( 90) covalent geometry : bond 0.00403 (23264) covalent geometry : angle 0.62339 (31663) *********************** 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 719 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 630 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6638 (tp) cc_final: 0.6421 (tp) REVERT: G 76 GLU cc_start: 0.7420 (tt0) cc_final: 0.7131 (pt0) REVERT: G 202 ASP cc_start: 0.8178 (p0) cc_final: 0.7966 (p0) REVERT: G 246 ASP cc_start: 0.7591 (m-30) cc_final: 0.7188 (m-30) REVERT: G 402 VAL cc_start: 0.4110 (OUTLIER) cc_final: 0.2523 (t) REVERT: E 15 TYR cc_start: 0.8565 (t80) cc_final: 0.8348 (t80) REVERT: E 94 CYS cc_start: 0.7697 (m) cc_final: 0.7251 (m) REVERT: E 114 CYS cc_start: 0.7260 (t) cc_final: 0.6703 (t) REVERT: E 304 ASN cc_start: 0.7548 (m110) cc_final: 0.7107 (m110) REVERT: E 311 ASP cc_start: 0.7750 (p0) cc_final: 0.7453 (p0) REVERT: E 319 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8102 (mmmt) REVERT: E 327 LYS cc_start: 0.7683 (mmmm) cc_final: 0.7414 (mmmm) REVERT: C 42 ASP cc_start: 0.7314 (p0) cc_final: 0.7035 (p0) REVERT: C 81 GLN cc_start: 0.8803 (mm110) cc_final: 0.8186 (mt0) REVERT: C 108 ASP cc_start: 0.7635 (m-30) cc_final: 0.7339 (m-30) REVERT: C 112 MET cc_start: 0.8562 (ttm) cc_final: 0.8161 (ttt) REVERT: C 157 ASP cc_start: 0.8241 (t0) cc_final: 0.8012 (t0) REVERT: C 205 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7947 (p) REVERT: C 313 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 45 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7840 (mm-30) REVERT: F 75 ASP cc_start: 0.8267 (t0) cc_final: 0.8021 (t70) REVERT: F 260 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6923 (mt-10) REVERT: F 308 TYR cc_start: 0.7332 (t80) cc_final: 0.7042 (t80) REVERT: F 315 ILE cc_start: 0.8152 (mp) cc_final: 0.7885 (mm) REVERT: F 402 VAL cc_start: 0.4301 (p) cc_final: 0.2729 (m) REVERT: B 9 TYR cc_start: 0.8230 (m-80) cc_final: 0.7884 (m-80) REVERT: B 28 HIS cc_start: 0.8304 (m90) cc_final: 0.7790 (m90) REVERT: B 130 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8215 (mtpp) REVERT: B 148 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 166 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 182 SER cc_start: 0.7991 (t) cc_final: 0.7739 (m) REVERT: B 216 GLN cc_start: 0.7483 (tt0) cc_final: 0.7139 (tt0) REVERT: B 231 LEU cc_start: 0.8889 (tp) cc_final: 0.8662 (tt) REVERT: B 276 ILE cc_start: 0.8700 (mp) cc_final: 0.8424 (mt) REVERT: A 21 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: A 31 ILE cc_start: 0.8403 (tp) cc_final: 0.7957 (tp) REVERT: A 53 TYR cc_start: 0.8367 (m-80) cc_final: 0.8040 (m-10) REVERT: A 62 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7900 (tttp) REVERT: A 65 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 100 LEU cc_start: 0.8371 (tp) cc_final: 0.8001 (tp) REVERT: A 124 SER cc_start: 0.8432 (t) cc_final: 0.7801 (p) REVERT: A 275 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7600 (mtm) REVERT: H 31 ASP cc_start: 0.7732 (m-30) cc_final: 0.7515 (m-30) REVERT: H 76 ASN cc_start: 0.8458 (t0) cc_final: 0.8064 (t0) REVERT: H 91 TYR cc_start: 0.7039 (m-80) cc_final: 0.6690 (m-80) REVERT: W 59 PHE cc_start: 0.7549 (m-80) cc_final: 0.7085 (m-80) REVERT: W 82 MET cc_start: 0.6454 (tpp) cc_final: 0.5633 (mmm) REVERT: V 54 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7817 (mtt180) outliers start: 89 outliers final: 64 residues processed: 672 average time/residue: 0.3619 time to fit residues: 384.7616 Evaluate side-chains 687 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 618 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 42 VAL 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 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 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 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 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 143 VAL 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 318 VAL 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 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 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 77 ILE Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE 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 290 LYS 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 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 209 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 140 optimal weight: 0.0370 chunk 87 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 284 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 341 GLN B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 HIS A 132 ASN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111664 restraints weight = 37311.023| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.25 r_work: 0.3328 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23319 Z= 0.124 Angle : 0.602 11.324 31783 Z= 0.309 Chirality : 0.044 0.219 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.429 63.987 3392 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.50 % Allowed : 17.63 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 2897 helix: -2.31 (0.58), residues: 66 sheet: 0.21 (0.15), residues: 1104 loop : -0.54 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 99 HIS 0.010 0.001 HIS C 141 PHE 0.026 0.001 PHE F 365 TYR 0.019 0.001 TYR B 238 ARG 0.008 0.000 ARG A 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 6) link_NAG-ASN : angle 0.78590 ( 18) link_BETA1-4 : bond 0.00316 ( 4) link_BETA1-4 : angle 1.42172 ( 12) hydrogen bonds : bond 0.02992 ( 776) hydrogen bonds : angle 5.70668 ( 1992) SS BOND : bond 0.00294 ( 45) SS BOND : angle 0.98239 ( 90) covalent geometry : bond 0.00280 (23264) covalent geometry : angle 0.60014 (31663) *********************** REFINEMENT MACRO_CYCLE 7 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 717 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 631 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6541 (tp) cc_final: 0.6268 (tp) REVERT: G 76 GLU cc_start: 0.7418 (tt0) cc_final: 0.7128 (pt0) REVERT: G 202 ASP cc_start: 0.8175 (p0) cc_final: 0.7962 (p0) REVERT: G 246 ASP cc_start: 0.7556 (m-30) cc_final: 0.7129 (m-30) REVERT: G 402 VAL cc_start: 0.3948 (OUTLIER) cc_final: 0.2353 (t) REVERT: E 15 TYR cc_start: 0.8543 (t80) cc_final: 0.8319 (t80) REVERT: E 94 CYS cc_start: 0.7654 (m) cc_final: 0.7235 (m) REVERT: E 304 ASN cc_start: 0.7487 (m110) cc_final: 0.7042 (m110) REVERT: E 319 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8092 (mmmt) REVERT: E 327 LYS cc_start: 0.7662 (mmmm) cc_final: 0.7268 (mmmm) REVERT: C 42 ASP cc_start: 0.7329 (p0) cc_final: 0.7032 (p0) REVERT: C 81 GLN cc_start: 0.8774 (mm110) cc_final: 0.8188 (mt0) REVERT: C 108 ASP cc_start: 0.7620 (m-30) cc_final: 0.7321 (m-30) REVERT: C 112 MET cc_start: 0.8559 (ttm) cc_final: 0.8193 (ttt) REVERT: C 157 ASP cc_start: 0.8208 (t0) cc_final: 0.7975 (t0) REVERT: C 205 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (p) REVERT: C 313 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7886 (mt-10) REVERT: F 45 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7748 (mm-30) REVERT: F 75 ASP cc_start: 0.8275 (t0) cc_final: 0.8028 (t70) REVERT: F 99 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: F 260 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6879 (mt-10) REVERT: F 308 TYR cc_start: 0.7303 (t80) cc_final: 0.6998 (t80) REVERT: F 315 ILE cc_start: 0.8157 (mp) cc_final: 0.7872 (mm) REVERT: F 402 VAL cc_start: 0.4953 (p) cc_final: 0.3332 (m) REVERT: B 9 TYR cc_start: 0.8237 (m-80) cc_final: 0.7930 (m-80) REVERT: B 28 HIS cc_start: 0.8341 (m90) cc_final: 0.7803 (m90) REVERT: B 112 MET cc_start: 0.8714 (ttt) cc_final: 0.8461 (ttp) REVERT: B 120 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7696 (ptm-80) REVERT: B 130 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8176 (mtpp) REVERT: B 141 HIS cc_start: 0.8166 (t-90) cc_final: 0.7954 (t70) REVERT: B 148 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 157 ASP cc_start: 0.8196 (t0) cc_final: 0.6938 (t0) REVERT: B 161 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7509 (mpt180) REVERT: B 166 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 182 SER cc_start: 0.7970 (t) cc_final: 0.7721 (m) REVERT: B 216 GLN cc_start: 0.7354 (tt0) cc_final: 0.7061 (tt0) REVERT: B 231 LEU cc_start: 0.8874 (tp) cc_final: 0.8656 (tt) REVERT: B 276 ILE cc_start: 0.8717 (mp) cc_final: 0.8391 (mt) REVERT: A 21 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7375 (mtp85) REVERT: A 31 ILE cc_start: 0.8387 (tp) cc_final: 0.7981 (tp) REVERT: A 53 TYR cc_start: 0.8315 (m-80) cc_final: 0.7989 (m-10) REVERT: A 62 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7986 (tttp) REVERT: A 100 LEU cc_start: 0.8408 (tp) cc_final: 0.8031 (tp) REVERT: A 124 SER cc_start: 0.8413 (t) cc_final: 0.7795 (p) REVERT: A 159 GLN cc_start: 0.8446 (pt0) cc_final: 0.8235 (pt0) REVERT: A 275 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7598 (mtm) REVERT: H 31 ASP cc_start: 0.7885 (m-30) cc_final: 0.7668 (m-30) REVERT: H 76 ASN cc_start: 0.8400 (t0) cc_final: 0.8022 (t0) REVERT: W 28 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7294 (ttp80) REVERT: W 59 PHE cc_start: 0.7548 (m-80) cc_final: 0.7219 (m-80) REVERT: W 82 MET cc_start: 0.6443 (tpp) cc_final: 0.5602 (mmm) REVERT: V 54 ARG cc_start: 0.7927 (mtt-85) cc_final: 0.7662 (mtt-85) outliers start: 86 outliers final: 59 residues processed: 672 average time/residue: 0.3333 time to fit residues: 350.5957 Evaluate side-chains 674 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 610 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 42 VAL 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 55 MET 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 159 VAL Chi-restraints excluded: chain E residue 171 THR 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 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 318 VAL 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 26 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 ILE 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 285 LEU Chi-restraints excluded: chain A residue 290 LYS 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 52 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 237 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 244 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 260 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 392 GLN E 102 GLN E 218 ASN ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS F 77 GLN F 157 ASN B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN 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 = 0.3646 r_free = 0.3646 target = 0.127394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111836 restraints weight = 37145.345| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.24 r_work: 0.3332 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23319 Z= 0.125 Angle : 0.596 11.323 31783 Z= 0.306 Chirality : 0.044 0.218 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.290 63.112 3392 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.30 % Allowed : 18.32 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2897 helix: -2.20 (0.60), residues: 66 sheet: 0.27 (0.15), residues: 1096 loop : -0.53 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 99 HIS 0.010 0.001 HIS C 141 PHE 0.022 0.001 PHE F 365 TYR 0.017 0.001 TYR G 320 ARG 0.008 0.000 ARG C 88 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 6) link_NAG-ASN : angle 0.75742 ( 18) link_BETA1-4 : bond 0.00261 ( 4) link_BETA1-4 : angle 1.41208 ( 12) hydrogen bonds : bond 0.02980 ( 776) hydrogen bonds : angle 5.57797 ( 1992) SS BOND : bond 0.00322 ( 45) SS BOND : angle 1.05331 ( 90) covalent geometry : bond 0.00281 (23264) covalent geometry : angle 0.59320 (31663) *********************** REFINEMENT MACRO_CYCLE 8 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 713 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 632 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6554 (tp) cc_final: 0.6236 (tp) REVERT: G 76 GLU cc_start: 0.7440 (tt0) cc_final: 0.7107 (pt0) REVERT: G 109 MET cc_start: 0.8615 (ptt) cc_final: 0.8310 (ptp) REVERT: G 152 THR cc_start: 0.8467 (m) cc_final: 0.8173 (t) REVERT: G 202 ASP cc_start: 0.8171 (p0) cc_final: 0.7965 (p0) REVERT: G 246 ASP cc_start: 0.7518 (m-30) cc_final: 0.7082 (m-30) REVERT: G 356 PHE cc_start: 0.7861 (p90) cc_final: 0.7632 (p90) REVERT: G 389 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8220 (t) REVERT: G 402 VAL cc_start: 0.3832 (OUTLIER) cc_final: 0.2147 (t) REVERT: E 15 TYR cc_start: 0.8520 (t80) cc_final: 0.8289 (t80) REVERT: E 94 CYS cc_start: 0.7651 (m) cc_final: 0.7228 (m) REVERT: E 304 ASN cc_start: 0.7471 (m110) cc_final: 0.6993 (m110) REVERT: E 311 ASP cc_start: 0.7759 (p0) cc_final: 0.7418 (p0) REVERT: E 319 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8090 (mmmt) REVERT: E 327 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7315 (mmmm) REVERT: C 42 ASP cc_start: 0.7341 (p0) cc_final: 0.7034 (p0) REVERT: C 81 GLN cc_start: 0.8767 (mm110) cc_final: 0.8208 (mt0) REVERT: C 108 ASP cc_start: 0.7516 (m-30) cc_final: 0.7202 (m-30) REVERT: C 112 MET cc_start: 0.8566 (ttm) cc_final: 0.8204 (ttt) REVERT: C 157 ASP cc_start: 0.8140 (t0) cc_final: 0.7856 (t0) REVERT: C 205 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7773 (p) REVERT: C 302 ASP cc_start: 0.7819 (p0) cc_final: 0.7617 (p0) REVERT: C 313 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7862 (mt-10) REVERT: F 45 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7652 (mm-30) REVERT: F 75 ASP cc_start: 0.8250 (t0) cc_final: 0.7978 (t70) REVERT: F 262 TYR cc_start: 0.8098 (m-80) cc_final: 0.7888 (m-10) REVERT: F 308 TYR cc_start: 0.7277 (t80) cc_final: 0.6943 (t80) REVERT: F 315 ILE cc_start: 0.8113 (mp) cc_final: 0.7821 (mm) REVERT: F 402 VAL cc_start: 0.4795 (p) cc_final: 0.3111 (m) REVERT: B 28 HIS cc_start: 0.8324 (m90) cc_final: 0.7792 (m90) REVERT: B 53 TYR cc_start: 0.8553 (m-80) cc_final: 0.8177 (m-80) REVERT: B 120 ARG cc_start: 0.7973 (ptm160) cc_final: 0.7683 (ptm-80) REVERT: B 130 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8183 (mtpp) REVERT: B 148 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 157 ASP cc_start: 0.8205 (t0) cc_final: 0.6868 (t0) REVERT: B 161 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7491 (mpt180) REVERT: B 166 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 182 SER cc_start: 0.7960 (t) cc_final: 0.7707 (m) REVERT: B 216 GLN cc_start: 0.7378 (tt0) cc_final: 0.7070 (tt0) REVERT: B 231 LEU cc_start: 0.8873 (tp) cc_final: 0.8654 (tt) REVERT: B 276 ILE cc_start: 0.8737 (mp) cc_final: 0.8432 (mt) REVERT: B 286 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8129 (mtpt) REVERT: A 21 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7356 (mtp85) REVERT: A 31 ILE cc_start: 0.8414 (tp) cc_final: 0.8057 (tp) REVERT: A 53 TYR cc_start: 0.8367 (m-80) cc_final: 0.8010 (m-10) REVERT: A 62 LYS cc_start: 0.8272 (ttmm) cc_final: 0.7981 (tttp) REVERT: A 100 LEU cc_start: 0.8377 (tp) cc_final: 0.8019 (tp) REVERT: A 124 SER cc_start: 0.8413 (t) cc_final: 0.7802 (p) REVERT: A 159 GLN cc_start: 0.8409 (pt0) cc_final: 0.8204 (pt0) REVERT: A 224 GLU cc_start: 0.7948 (tp30) cc_final: 0.7556 (mp0) REVERT: A 275 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7580 (mtm) REVERT: H 31 ASP cc_start: 0.7878 (m-30) cc_final: 0.7667 (m-30) REVERT: H 76 ASN cc_start: 0.8361 (t0) cc_final: 0.8002 (t0) REVERT: W 28 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7178 (ttp80) REVERT: W 59 PHE cc_start: 0.7513 (m-80) cc_final: 0.7231 (m-80) REVERT: W 82 MET cc_start: 0.6506 (tpp) cc_final: 0.5797 (mmm) outliers start: 81 outliers final: 67 residues processed: 672 average time/residue: 0.3310 time to fit residues: 347.7912 Evaluate side-chains 690 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 618 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 42 VAL 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 29 ILE Chi-restraints excluded: chain E residue 42 VAL 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 96 CYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR 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 329 VAL 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 78 CYS Chi-restraints excluded: chain F residue 99 GLU 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 246 ASP Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 318 VAL 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 B residue 341 GLN 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 26 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 276 ILE 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 A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain V residue 2 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 274 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 155 optimal weight: 0.0060 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 157 ASN B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111965 restraints weight = 37273.579| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.24 r_work: 0.3333 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23319 Z= 0.128 Angle : 0.605 12.885 31783 Z= 0.310 Chirality : 0.044 0.213 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.240 63.097 3392 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 3.34 % Allowed : 18.85 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2897 helix: -2.27 (0.58), residues: 66 sheet: 0.27 (0.15), residues: 1107 loop : -0.49 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 47 HIS 0.010 0.001 HIS C 141 PHE 0.028 0.001 PHE B 259 TYR 0.016 0.001 TYR G 320 ARG 0.007 0.000 ARG B 88 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 6) link_NAG-ASN : angle 0.76529 ( 18) link_BETA1-4 : bond 0.00292 ( 4) link_BETA1-4 : angle 1.41062 ( 12) hydrogen bonds : bond 0.02955 ( 776) hydrogen bonds : angle 5.53521 ( 1992) SS BOND : bond 0.00284 ( 45) SS BOND : angle 0.99161 ( 90) covalent geometry : bond 0.00289 (23264) covalent geometry : angle 0.60327 (31663) *********************** REFINEMENT MACRO_CYCLE 9 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 705 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 623 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6577 (tp) cc_final: 0.6235 (tp) REVERT: G 76 GLU cc_start: 0.7456 (tt0) cc_final: 0.7115 (pt0) REVERT: G 152 THR cc_start: 0.8480 (m) cc_final: 0.8182 (t) REVERT: G 202 ASP cc_start: 0.8171 (p0) cc_final: 0.7966 (p0) REVERT: G 246 ASP cc_start: 0.7515 (m-30) cc_final: 0.7103 (m-30) REVERT: G 356 PHE cc_start: 0.7848 (p90) cc_final: 0.7602 (p90) REVERT: G 389 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8230 (t) REVERT: G 402 VAL cc_start: 0.3759 (OUTLIER) cc_final: 0.2131 (t) REVERT: E 5 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7657 (p) REVERT: E 15 TYR cc_start: 0.8524 (t80) cc_final: 0.8288 (t80) REVERT: E 94 CYS cc_start: 0.7645 (m) cc_final: 0.7223 (m) REVERT: E 304 ASN cc_start: 0.7474 (m110) cc_final: 0.7027 (m110) REVERT: E 311 ASP cc_start: 0.7744 (p0) cc_final: 0.7423 (p0) REVERT: E 319 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8116 (mmmt) REVERT: C 42 ASP cc_start: 0.7348 (p0) cc_final: 0.7057 (p0) REVERT: C 81 GLN cc_start: 0.8756 (mm110) cc_final: 0.8204 (mt0) REVERT: C 108 ASP cc_start: 0.7517 (m-30) cc_final: 0.7205 (m-30) REVERT: C 112 MET cc_start: 0.8567 (ttm) cc_final: 0.8214 (ttt) REVERT: C 130 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8272 (ptpp) REVERT: C 157 ASP cc_start: 0.8123 (t0) cc_final: 0.7846 (t0) REVERT: C 205 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7739 (p) REVERT: C 216 GLN cc_start: 0.7246 (tp-100) cc_final: 0.6796 (tp-100) REVERT: C 302 ASP cc_start: 0.7778 (p0) cc_final: 0.7566 (p0) REVERT: C 313 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7835 (mt-10) REVERT: F 45 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7734 (mm-30) REVERT: F 75 ASP cc_start: 0.8270 (t0) cc_final: 0.7989 (t70) REVERT: F 99 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 157 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7487 (t0) REVERT: F 262 TYR cc_start: 0.8112 (m-80) cc_final: 0.7892 (m-10) REVERT: F 308 TYR cc_start: 0.7263 (t80) cc_final: 0.6892 (t80) REVERT: F 315 ILE cc_start: 0.8110 (mp) cc_final: 0.7823 (mm) REVERT: F 402 VAL cc_start: 0.4786 (p) cc_final: 0.3098 (m) REVERT: B 28 HIS cc_start: 0.8316 (m90) cc_final: 0.7834 (m90) REVERT: B 94 ASP cc_start: 0.7584 (t0) cc_final: 0.7334 (t0) REVERT: B 112 MET cc_start: 0.8791 (ttt) cc_final: 0.8518 (ttp) REVERT: B 120 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7683 (ptm-80) REVERT: B 130 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8207 (mtpp) REVERT: B 148 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7482 (mm-30) REVERT: B 157 ASP cc_start: 0.8207 (t0) cc_final: 0.6856 (t0) REVERT: B 161 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7469 (mpt180) REVERT: B 166 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 182 SER cc_start: 0.7971 (t) cc_final: 0.7716 (m) REVERT: B 216 GLN cc_start: 0.7379 (tt0) cc_final: 0.7084 (tt0) REVERT: B 231 LEU cc_start: 0.8877 (tp) cc_final: 0.8664 (tt) REVERT: B 276 ILE cc_start: 0.8715 (mp) cc_final: 0.8433 (mt) REVERT: B 286 LYS cc_start: 0.8333 (mtpt) cc_final: 0.8110 (mtpt) REVERT: A 21 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7622 (mtp85) REVERT: A 31 ILE cc_start: 0.8408 (tp) cc_final: 0.8110 (tp) REVERT: A 53 TYR cc_start: 0.8363 (m-80) cc_final: 0.7887 (m-10) REVERT: A 62 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7996 (tttp) REVERT: A 100 LEU cc_start: 0.8431 (tp) cc_final: 0.7988 (tp) REVERT: A 124 SER cc_start: 0.8407 (t) cc_final: 0.7812 (p) REVERT: A 216 GLN cc_start: 0.8055 (tt0) cc_final: 0.7685 (tt0) REVERT: A 275 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7536 (mtm) REVERT: H 76 ASN cc_start: 0.8351 (t0) cc_final: 0.7987 (t0) REVERT: W 28 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7161 (ttp80) REVERT: W 82 MET cc_start: 0.6518 (tpp) cc_final: 0.5831 (mmm) REVERT: V 54 ARG cc_start: 0.7859 (mtt-85) cc_final: 0.7551 (mtt180) outliers start: 82 outliers final: 67 residues processed: 664 average time/residue: 0.3436 time to fit residues: 356.7138 Evaluate side-chains 696 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 621 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 42 VAL 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 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 133 LEU 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 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 329 VAL 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 78 CYS Chi-restraints excluded: chain F residue 99 GLU 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 207 THR Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 318 VAL 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 B residue 341 GLN 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 26 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 276 ILE 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 A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain V residue 2 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 174 optimal weight: 0.0170 chunk 209 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 186 optimal weight: 3.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 140 HIS ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111205 restraints weight = 37311.281| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.25 r_work: 0.3323 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23319 Z= 0.152 Angle : 0.616 13.491 31783 Z= 0.316 Chirality : 0.044 0.216 3490 Planarity : 0.005 0.047 4104 Dihedral : 5.292 64.352 3392 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 3.30 % Allowed : 19.22 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2897 helix: -1.28 (0.73), residues: 48 sheet: 0.19 (0.15), residues: 1118 loop : -0.50 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 99 HIS 0.011 0.001 HIS C 141 PHE 0.026 0.002 PHE X 67 TYR 0.016 0.001 TYR G 320 ARG 0.009 0.000 ARG A 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 6) link_NAG-ASN : angle 0.75710 ( 18) link_BETA1-4 : bond 0.00267 ( 4) link_BETA1-4 : angle 1.42943 ( 12) hydrogen bonds : bond 0.03022 ( 776) hydrogen bonds : angle 5.50373 ( 1992) SS BOND : bond 0.00324 ( 45) SS BOND : angle 1.04602 ( 90) covalent geometry : bond 0.00342 (23264) covalent geometry : angle 0.61328 (31663) ********************** REFINEMENT MACRO_CYCLE 10 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 712 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 631 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6594 (tp) cc_final: 0.6254 (tp) REVERT: G 76 GLU cc_start: 0.7556 (tt0) cc_final: 0.7183 (pt0) REVERT: G 109 MET cc_start: 0.8633 (ptt) cc_final: 0.8344 (ptp) REVERT: G 202 ASP cc_start: 0.8168 (p0) cc_final: 0.7963 (p0) REVERT: G 246 ASP cc_start: 0.7541 (m-30) cc_final: 0.7127 (m-30) REVERT: G 356 PHE cc_start: 0.7866 (p90) cc_final: 0.7608 (p90) REVERT: G 389 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8256 (t) REVERT: G 402 VAL cc_start: 0.3867 (OUTLIER) cc_final: 0.2220 (t) REVERT: E 5 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7681 (p) REVERT: E 15 TYR cc_start: 0.8520 (t80) cc_final: 0.8282 (t80) REVERT: E 94 CYS cc_start: 0.7685 (m) cc_final: 0.7246 (m) REVERT: E 114 CYS cc_start: 0.7067 (t) cc_final: 0.6466 (t) REVERT: E 311 ASP cc_start: 0.7736 (p0) cc_final: 0.7437 (p0) REVERT: E 319 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8112 (mmmt) REVERT: C 42 ASP cc_start: 0.7340 (p0) cc_final: 0.7062 (p0) REVERT: C 81 GLN cc_start: 0.8772 (mm110) cc_final: 0.8223 (mt0) REVERT: C 108 ASP cc_start: 0.7594 (m-30) cc_final: 0.7289 (m-30) REVERT: C 112 MET cc_start: 0.8580 (ttm) cc_final: 0.8227 (ttt) REVERT: C 130 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8289 (ptpp) REVERT: C 157 ASP cc_start: 0.8107 (t0) cc_final: 0.7835 (t0) REVERT: C 205 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (p) REVERT: C 216 GLN cc_start: 0.7263 (tp-100) cc_final: 0.6811 (tp-100) REVERT: C 313 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 45 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7768 (mm-30) REVERT: F 75 ASP cc_start: 0.8277 (t0) cc_final: 0.8008 (t70) REVERT: F 99 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: F 157 ASN cc_start: 0.7922 (t0) cc_final: 0.7562 (t0) REVERT: F 260 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7037 (mt-10) REVERT: F 262 TYR cc_start: 0.8141 (m-80) cc_final: 0.7907 (m-10) REVERT: F 308 TYR cc_start: 0.7273 (t80) cc_final: 0.6992 (t80) REVERT: F 315 ILE cc_start: 0.8115 (mp) cc_final: 0.7835 (mm) REVERT: F 402 VAL cc_start: 0.4849 (p) cc_final: 0.3164 (m) REVERT: B 28 HIS cc_start: 0.8327 (m90) cc_final: 0.7795 (m90) REVERT: B 53 TYR cc_start: 0.8547 (m-80) cc_final: 0.8234 (m-80) REVERT: B 94 ASP cc_start: 0.7638 (t0) cc_final: 0.7380 (t0) REVERT: B 120 ARG cc_start: 0.7986 (ptm160) cc_final: 0.7730 (ptm-80) REVERT: B 157 ASP cc_start: 0.8198 (t0) cc_final: 0.6827 (t0) REVERT: B 161 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7440 (mpt180) REVERT: B 166 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7234 (mm-30) REVERT: B 182 SER cc_start: 0.7956 (t) cc_final: 0.7703 (m) REVERT: B 216 GLN cc_start: 0.7416 (tt0) cc_final: 0.7087 (tt0) REVERT: B 231 LEU cc_start: 0.8869 (tp) cc_final: 0.8644 (tt) REVERT: B 276 ILE cc_start: 0.8682 (mp) cc_final: 0.8374 (mt) REVERT: A 21 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7323 (mtp85) REVERT: A 31 ILE cc_start: 0.8406 (tp) cc_final: 0.8100 (tp) REVERT: A 53 TYR cc_start: 0.8278 (m-80) cc_final: 0.7907 (m-10) REVERT: A 62 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8002 (tttp) REVERT: A 100 LEU cc_start: 0.8425 (tp) cc_final: 0.7948 (tp) REVERT: A 124 SER cc_start: 0.8418 (t) cc_final: 0.7822 (p) REVERT: A 216 GLN cc_start: 0.8050 (tt0) cc_final: 0.7698 (tt0) REVERT: A 275 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7519 (mtm) REVERT: H 31 ASP cc_start: 0.7789 (m-30) cc_final: 0.7408 (t0) REVERT: H 76 ASN cc_start: 0.8322 (t0) cc_final: 0.7950 (t0) REVERT: W 28 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7124 (ttp80) outliers start: 81 outliers final: 68 residues processed: 672 average time/residue: 0.3502 time to fit residues: 369.3133 Evaluate side-chains 699 residues out of total 2456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 624 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 18 ILE Chi-restraints excluded: chain G residue 42 VAL 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 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR 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 55 MET 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 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 202 ASP 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 329 VAL 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 78 CYS Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 GLU 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 246 ASP Chi-restraints excluded: chain F residue 263 THR Chi-restraints excluded: chain F residue 318 VAL 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 8 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 276 ILE 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 A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain V residue 2 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 233 optimal weight: 0.0040 chunk 198 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111807 restraints weight = 37241.447| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.26 r_work: 0.3332 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23319 Z= 0.131 Angle : 0.608 13.705 31783 Z= 0.311 Chirality : 0.044 0.213 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.220 63.720 3392 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.97 % Allowed : 19.50 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2897 helix: -1.25 (0.73), residues: 48 sheet: 0.13 (0.15), residues: 1154 loop : -0.45 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 99 HIS 0.010 0.001 HIS C 141 PHE 0.025 0.001 PHE X 67 TYR 0.016 0.001 TYR G 320 ARG 0.013 0.000 ARG A 120 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 6) link_NAG-ASN : angle 0.80220 ( 18) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.38290 ( 12) hydrogen bonds : bond 0.02927 ( 776) hydrogen bonds : angle 5.44263 ( 1992) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.01478 ( 90) covalent geometry : bond 0.00295 (23264) covalent geometry : angle 0.60549 (31663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13738.92 seconds wall clock time: 236 minutes 0.27 seconds (14160.27 seconds total)