Starting phenix.real_space_refine on Fri Mar 6 06:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bok_30131/03_2026/7bok_30131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bok_30131/03_2026/7bok_30131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bok_30131/03_2026/7bok_30131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bok_30131/03_2026/7bok_30131.map" model { file = "/net/cci-nas-00/data/ceres_data/7bok_30131/03_2026/7bok_30131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bok_30131/03_2026/7bok_30131.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 108 5.16 5 C 18480 2.51 5 N 4848 2.21 5 O 5664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29112 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "B" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "C" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "D" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "E" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "F" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "H" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "I" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "J" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "K" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "L" Number of atoms: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2383 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 24, 'TRANS': 284} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.04, per 1000 atoms: 0.24 Number of scatterers: 29112 At special positions: 0 Unit cell: (184.08, 115.44, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 108 16.00 O 5664 8.00 N 4848 7.00 C 18480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 58 sheets defined 36.2% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.811A pdb=" N VAL A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.641A pdb=" N ARG A 54 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.758A pdb=" N ALA A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 219 through 225 removed outlier: 4.008A pdb=" N VAL A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR A 265 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.585A pdb=" N VAL B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.942A pdb=" N ALA B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 removed outlier: 3.758A pdb=" N ALA B 171 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR B 265 " --> pdb=" O THR B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.586A pdb=" N VAL C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 47 removed outlier: 4.511A pdb=" N GLY C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.942A pdb=" N ALA C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA C 171 " --> pdb=" O PRO C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 219 through 225 removed outlier: 3.979A pdb=" N VAL C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.586A pdb=" N VAL D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA D 171 " --> pdb=" O PRO D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 removed outlier: 3.590A pdb=" N SER D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 300 through 306 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.585A pdb=" N VAL E 32 " --> pdb=" O GLN E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY E 41 " --> pdb=" O PRO E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA E 171 " --> pdb=" O PRO E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL E 225 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 300 through 306 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.585A pdb=" N VAL F 32 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.641A pdb=" N ARG F 54 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU F 119 " --> pdb=" O THR F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA F 171 " --> pdb=" O PRO F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL F 225 " --> pdb=" O VAL F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR F 265 " --> pdb=" O THR F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 300 through 306 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.811A pdb=" N VAL G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY G 41 " --> pdb=" O PRO G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.641A pdb=" N ARG G 54 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 removed outlier: 3.758A pdb=" N ALA G 171 " --> pdb=" O PRO G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 201 Processing helix chain 'G' and resid 219 through 225 removed outlier: 4.008A pdb=" N VAL G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR G 265 " --> pdb=" O THR G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 287 Processing helix chain 'G' and resid 300 through 306 Processing helix chain 'H' and resid 28 through 36 removed outlier: 3.585A pdb=" N VAL H 32 " --> pdb=" O GLN H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY H 41 " --> pdb=" O PRO H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG H 54 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 162 removed outlier: 3.942A pdb=" N ALA H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 171 removed outlier: 3.758A pdb=" N ALA H 171 " --> pdb=" O PRO H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER H 190 " --> pdb=" O ALA H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 201 Processing helix chain 'H' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL H 225 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR H 265 " --> pdb=" O THR H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 287 Processing helix chain 'H' and resid 300 through 306 Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.586A pdb=" N VAL I 32 " --> pdb=" O GLN I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 47 removed outlier: 4.511A pdb=" N GLY I 41 " --> pdb=" O PRO I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG I 54 " --> pdb=" O PRO I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU I 119 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 162 removed outlier: 3.942A pdb=" N ALA I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA I 171 " --> pdb=" O PRO I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER I 190 " --> pdb=" O ALA I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 201 Processing helix chain 'I' and resid 219 through 225 removed outlier: 3.979A pdb=" N VAL I 225 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR I 265 " --> pdb=" O THR I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 287 Processing helix chain 'I' and resid 300 through 306 Processing helix chain 'J' and resid 28 through 36 removed outlier: 3.586A pdb=" N VAL J 32 " --> pdb=" O GLN J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY J 41 " --> pdb=" O PRO J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG J 54 " --> pdb=" O PRO J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU J 119 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA J 171 " --> pdb=" O PRO J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 191 removed outlier: 3.590A pdb=" N SER J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 192 through 201 Processing helix chain 'J' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL J 225 " --> pdb=" O VAL J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR J 265 " --> pdb=" O THR J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 287 Processing helix chain 'J' and resid 300 through 306 Processing helix chain 'K' and resid 28 through 36 removed outlier: 3.585A pdb=" N VAL K 32 " --> pdb=" O GLN K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY K 41 " --> pdb=" O PRO K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 54 removed outlier: 3.640A pdb=" N ARG K 54 " --> pdb=" O PRO K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU K 119 " --> pdb=" O THR K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA K 171 " --> pdb=" O PRO K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 201 Processing helix chain 'K' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL K 225 " --> pdb=" O VAL K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR K 265 " --> pdb=" O THR K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 287 Processing helix chain 'K' and resid 300 through 306 Processing helix chain 'L' and resid 28 through 36 removed outlier: 3.585A pdb=" N VAL L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 47 removed outlier: 4.512A pdb=" N GLY L 41 " --> pdb=" O PRO L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 54 removed outlier: 3.641A pdb=" N ARG L 54 " --> pdb=" O PRO L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 106 through 119 removed outlier: 4.107A pdb=" N CYS L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU L 119 " --> pdb=" O THR L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 154 through 162 removed outlier: 3.943A pdb=" N ALA L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 171 removed outlier: 3.759A pdb=" N ALA L 171 " --> pdb=" O PRO L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 191 removed outlier: 3.591A pdb=" N SER L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 192 through 201 Processing helix chain 'L' and resid 219 through 225 removed outlier: 3.980A pdb=" N VAL L 225 " --> pdb=" O VAL L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 273 removed outlier: 4.043A pdb=" N THR L 265 " --> pdb=" O THR L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 287 Processing helix chain 'L' and resid 300 through 306 Processing sheet with id=1, first strand: chain 'A' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR A 131 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR A 23 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE A 127 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=3, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=4, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=5, first strand: chain 'B' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR B 131 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR B 23 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE B 127 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=7, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=8, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=9, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE B 226 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR C 131 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 23 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE C 127 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=12, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=13, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=14, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE C 226 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR D 131 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR D 23 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE D 127 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=17, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=18, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=19, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE D 226 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'E' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR E 131 " --> pdb=" O PHE E 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR E 23 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE E 127 " --> pdb=" O THR E 23 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=22, first strand: chain 'E' and resid 237 through 238 Processing sheet with id=23, first strand: chain 'E' and resid 237 through 238 Processing sheet with id=24, first strand: chain 'E' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE E 226 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'F' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR F 131 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR F 23 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE F 127 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=27, first strand: chain 'F' and resid 237 through 238 Processing sheet with id=28, first strand: chain 'F' and resid 237 through 238 Processing sheet with id=29, first strand: chain 'F' and resid 226 through 227 removed outlier: 4.575A pdb=" N ILE F 226 " --> pdb=" O LEU F 234 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'G' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR G 131 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR G 23 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE G 127 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'G' and resid 84 through 85 Processing sheet with id=32, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=33, first strand: chain 'G' and resid 237 through 238 Processing sheet with id=34, first strand: chain 'H' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR H 131 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR H 23 " --> pdb=" O ILE H 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE H 127 " --> pdb=" O THR H 23 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'H' and resid 84 through 85 Processing sheet with id=36, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=37, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=38, first strand: chain 'H' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE H 226 " --> pdb=" O LEU H 234 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'I' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR I 131 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR I 23 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE I 127 " --> pdb=" O THR I 23 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'I' and resid 84 through 85 Processing sheet with id=41, first strand: chain 'I' and resid 237 through 238 Processing sheet with id=42, first strand: chain 'I' and resid 237 through 238 Processing sheet with id=43, first strand: chain 'I' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE I 226 " --> pdb=" O LEU I 234 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'J' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR J 131 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR J 23 " --> pdb=" O ILE J 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE J 127 " --> pdb=" O THR J 23 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'J' and resid 84 through 85 Processing sheet with id=46, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=47, first strand: chain 'J' and resid 237 through 238 Processing sheet with id=48, first strand: chain 'J' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE J 226 " --> pdb=" O LEU J 234 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'K' and resid 56 through 61 removed outlier: 3.522A pdb=" N THR K 131 " --> pdb=" O PHE K 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR K 23 " --> pdb=" O ILE K 127 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE K 127 " --> pdb=" O THR K 23 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'K' and resid 84 through 85 Processing sheet with id=51, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=52, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=53, first strand: chain 'K' and resid 226 through 227 removed outlier: 4.576A pdb=" N ILE K 226 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'L' and resid 56 through 61 removed outlier: 3.523A pdb=" N THR L 131 " --> pdb=" O PHE L 19 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR L 23 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE L 127 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'L' and resid 84 through 85 Processing sheet with id=56, first strand: chain 'L' and resid 237 through 238 Processing sheet with id=57, first strand: chain 'L' and resid 237 through 238 Processing sheet with id=58, first strand: chain 'L' and resid 226 through 227 removed outlier: 4.575A pdb=" N ILE L 226 " --> pdb=" O LEU L 234 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 2874 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: 6.03 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 12468 1.40 - 1.57: 17208 1.57 - 1.75: 0 1.75 - 1.93: 204 1.93 - 2.10: 36 Bond restraints: 29916 Sorted by residual: bond pdb=" C3B HEM J 401 " pdb=" CAB HEM J 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM D 401 " pdb=" CAB HEM D 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM A 401 " pdb=" CAB HEM A 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM G 401 " pdb=" CAB HEM G 401 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3B HEM E 401 " pdb=" CAB HEM E 401 " ideal model delta sigma weight residual 1.544 1.469 0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 29911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 37294 1.42 - 2.85: 2722 2.85 - 4.27: 660 4.27 - 5.70: 170 5.70 - 7.12: 98 Bond angle restraints: 40944 Sorted by residual: angle pdb=" N VAL C 193 " pdb=" CA VAL C 193 " pdb=" C VAL C 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" N VAL I 193 " pdb=" CA VAL I 193 " pdb=" C VAL I 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.63e+01 angle pdb=" N VAL D 193 " pdb=" CA VAL D 193 " pdb=" C VAL D 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.62e+01 angle pdb=" N VAL J 193 " pdb=" CA VAL J 193 " pdb=" C VAL J 193 " ideal model delta sigma weight residual 110.42 116.95 -6.53 9.60e-01 1.09e+00 4.62e+01 angle pdb=" N VAL E 193 " pdb=" CA VAL E 193 " pdb=" C VAL E 193 " ideal model delta sigma weight residual 110.62 117.07 -6.45 1.02e+00 9.61e-01 4.00e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 15906 17.22 - 34.43: 1254 34.43 - 51.65: 314 51.65 - 68.86: 22 68.86 - 86.08: 72 Dihedral angle restraints: 17568 sinusoidal: 7032 harmonic: 10536 Sorted by residual: dihedral pdb=" C2B HEM A 401 " pdb=" C3B HEM A 401 " pdb=" CAB HEM A 401 " pdb=" CBB HEM A 401 " ideal model delta sinusoidal sigma weight residual 180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C2B HEM G 401 " pdb=" C3B HEM G 401 " pdb=" CAB HEM G 401 " pdb=" CBB HEM G 401 " ideal model delta sinusoidal sigma weight residual -180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C2B HEM E 401 " pdb=" C3B HEM E 401 " pdb=" CAB HEM E 401 " pdb=" CBB HEM E 401 " ideal model delta sinusoidal sigma weight residual -180.00 -111.02 -68.98 2 1.00e+01 1.00e-02 4.18e+01 ... (remaining 17565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3242 0.055 - 0.110: 1018 0.110 - 0.165: 118 0.165 - 0.220: 0 0.220 - 0.275: 14 Chirality restraints: 4392 Sorted by residual: chirality pdb=" CA VAL G 225 " pdb=" N VAL G 225 " pdb=" C VAL G 225 " pdb=" CB VAL G 225 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE B 256 " pdb=" CA ILE B 256 " pdb=" CG1 ILE B 256 " pdb=" CG2 ILE B 256 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 4389 not shown) Planarity restraints: 5484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEM G 401 " -0.034 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" CGD HEM G 401 " 0.114 2.00e-02 2.50e+03 pdb=" O1D HEM G 401 " -0.041 2.00e-02 2.50e+03 pdb=" O2D HEM G 401 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM A 401 " 0.034 2.00e-02 2.50e+03 6.61e-02 4.37e+01 pdb=" CGD HEM A 401 " -0.114 2.00e-02 2.50e+03 pdb=" O1D HEM A 401 " 0.041 2.00e-02 2.50e+03 pdb=" O2D HEM A 401 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEM J 401 " -0.033 2.00e-02 2.50e+03 6.61e-02 4.36e+01 pdb=" CGD HEM J 401 " 0.114 2.00e-02 2.50e+03 pdb=" O1D HEM J 401 " -0.041 2.00e-02 2.50e+03 pdb=" O2D HEM J 401 " -0.040 2.00e-02 2.50e+03 ... (remaining 5481 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 353 2.61 - 3.18: 24281 3.18 - 3.75: 47946 3.75 - 4.33: 67427 4.33 - 4.90: 108595 Nonbonded interactions: 248602 Sorted by model distance: nonbonded pdb=" NH1 ARG F 198 " pdb=" CA SER I 187 " model vdw 2.036 3.550 nonbonded pdb=" CA SER C 187 " pdb=" NH1 ARG L 198 " model vdw 2.036 3.550 nonbonded pdb=" OG1 THR C 149 " pdb=" O ARG E 44 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR I 149 " pdb=" O ARG K 44 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR G 149 " pdb=" O ARG I 44 " model vdw 2.257 3.040 ... (remaining 248597 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.880 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.620 29928 Z= 0.361 Angle : 0.923 7.121 40944 Z= 0.496 Chirality : 0.051 0.275 4392 Planarity : 0.009 0.066 5484 Dihedral : 14.399 86.079 10800 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.13), residues: 3684 helix: -3.40 (0.12), residues: 996 sheet: -2.20 (0.19), residues: 876 loop : -1.46 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 238 TYR 0.009 0.002 TYR E 255 PHE 0.010 0.002 PHE C 303 TRP 0.010 0.002 TRP H 66 HIS 0.004 0.001 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00885 (29916) covalent geometry : angle 0.92298 (40944) hydrogen bonds : bond 0.20984 ( 1114) hydrogen bonds : angle 9.02171 ( 2874) Misc. bond : bond 0.61987 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8628 (mt) cc_final: 0.7045 (mt) REVERT: A 281 THR cc_start: 0.7158 (m) cc_final: 0.6709 (m) REVERT: B 206 ASP cc_start: 0.8391 (p0) cc_final: 0.8055 (p0) REVERT: B 240 ASN cc_start: 0.8572 (m-40) cc_final: 0.8356 (m-40) REVERT: C 139 ASN cc_start: 0.8480 (m-40) cc_final: 0.8155 (m-40) REVERT: C 240 ASN cc_start: 0.8422 (m-40) cc_final: 0.7940 (m110) REVERT: D 53 LYS cc_start: 0.8370 (mttt) cc_final: 0.7982 (mttt) REVERT: D 155 ASN cc_start: 0.7069 (t0) cc_final: 0.6864 (p0) REVERT: D 175 TYR cc_start: 0.8197 (m-80) cc_final: 0.7991 (m-80) REVERT: D 226 ILE cc_start: 0.8832 (mt) cc_final: 0.8570 (pt) REVERT: E 181 TYR cc_start: 0.8163 (m-80) cc_final: 0.7936 (m-80) REVERT: G 182 LEU cc_start: 0.8624 (mt) cc_final: 0.7044 (mt) REVERT: G 281 THR cc_start: 0.7153 (m) cc_final: 0.6701 (m) REVERT: H 206 ASP cc_start: 0.8389 (p0) cc_final: 0.8052 (p0) REVERT: H 240 ASN cc_start: 0.8573 (m-40) cc_final: 0.8356 (m-40) REVERT: I 139 ASN cc_start: 0.8481 (m-40) cc_final: 0.8155 (m-40) REVERT: I 240 ASN cc_start: 0.8410 (m-40) cc_final: 0.7934 (m110) REVERT: J 53 LYS cc_start: 0.8364 (mttt) cc_final: 0.7986 (mttt) REVERT: J 155 ASN cc_start: 0.7070 (t0) cc_final: 0.6865 (p0) REVERT: J 175 TYR cc_start: 0.8192 (m-80) cc_final: 0.7985 (m-80) REVERT: J 226 ILE cc_start: 0.8830 (mt) cc_final: 0.8564 (pt) REVERT: K 181 TYR cc_start: 0.8168 (m-80) cc_final: 0.7938 (m-80) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.2254 time to fit residues: 225.4263 Evaluate side-chains 273 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 HIS ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.074986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.066214 restraints weight = 94443.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068123 restraints weight = 48163.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069431 restraints weight = 29996.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.070311 restraints weight = 21061.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070916 restraints weight = 16157.174| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 29928 Z= 0.209 Angle : 0.697 6.417 40944 Z= 0.350 Chirality : 0.044 0.191 4392 Planarity : 0.006 0.050 5484 Dihedral : 9.958 89.566 4056 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.91 % Allowed : 13.91 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.13), residues: 3684 helix: -1.93 (0.14), residues: 1056 sheet: -1.81 (0.19), residues: 828 loop : -0.86 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 198 TYR 0.012 0.002 TYR B 181 PHE 0.018 0.001 PHE C 111 TRP 0.010 0.001 TRP G 188 HIS 0.009 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00564 (29916) covalent geometry : angle 0.69737 (40944) hydrogen bonds : bond 0.04186 ( 1114) hydrogen bonds : angle 6.43313 ( 2874) Misc. bond : bond 0.04187 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 THR cc_start: 0.7061 (m) cc_final: 0.6692 (m) REVERT: B 46 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.8492 (tp) REVERT: B 185 MET cc_start: 0.8349 (mmp) cc_final: 0.8091 (mmp) REVERT: B 241 MET cc_start: 0.8747 (mmm) cc_final: 0.8355 (mmm) REVERT: C 143 MET cc_start: 0.8526 (mmt) cc_final: 0.8204 (mmt) REVERT: C 240 ASN cc_start: 0.8219 (m-40) cc_final: 0.8012 (m-40) REVERT: D 155 ASN cc_start: 0.7349 (t0) cc_final: 0.6900 (p0) REVERT: G 281 THR cc_start: 0.7067 (m) cc_final: 0.6699 (m) REVERT: H 46 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.8492 (tp) REVERT: H 185 MET cc_start: 0.8336 (mmp) cc_final: 0.8080 (mmp) REVERT: H 241 MET cc_start: 0.8728 (mmm) cc_final: 0.8354 (mmm) REVERT: I 143 MET cc_start: 0.8512 (mmt) cc_final: 0.8192 (mmt) REVERT: I 240 ASN cc_start: 0.8216 (m-40) cc_final: 0.8016 (m-40) REVERT: J 155 ASN cc_start: 0.7343 (t0) cc_final: 0.6902 (p0) outliers start: 59 outliers final: 31 residues processed: 359 average time/residue: 0.2010 time to fit residues: 114.6845 Evaluate side-chains 280 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 261 optimal weight: 0.0170 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 329 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS D 224 ASN E 224 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067358 restraints weight = 93806.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069278 restraints weight = 47471.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070603 restraints weight = 29484.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071475 restraints weight = 20629.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072084 restraints weight = 15863.501| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 29928 Z= 0.131 Angle : 0.623 6.991 40944 Z= 0.306 Chirality : 0.042 0.163 4392 Planarity : 0.005 0.043 5484 Dihedral : 9.513 86.272 4056 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.88 % Allowed : 14.40 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 3684 helix: -1.03 (0.14), residues: 1092 sheet: -1.52 (0.19), residues: 828 loop : -0.51 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 267 TYR 0.012 0.001 TYR K 181 PHE 0.012 0.001 PHE I 251 TRP 0.004 0.001 TRP G 188 HIS 0.017 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00379 (29916) covalent geometry : angle 0.62347 (40944) hydrogen bonds : bond 0.03278 ( 1114) hydrogen bonds : angle 5.78638 ( 2874) Misc. bond : bond 0.02955 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 300 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 ASP cc_start: 0.6920 (m-30) cc_final: 0.6505 (t0) REVERT: B 179 GLN cc_start: 0.8985 (tt0) cc_final: 0.8707 (mt0) REVERT: B 181 TYR cc_start: 0.8458 (m-80) cc_final: 0.8212 (m-80) REVERT: C 240 ASN cc_start: 0.8171 (m-40) cc_final: 0.7922 (m-40) REVERT: D 143 MET cc_start: 0.8595 (mmt) cc_final: 0.8179 (mmt) REVERT: D 155 ASN cc_start: 0.7551 (t0) cc_final: 0.6969 (p0) REVERT: E 10 LEU cc_start: 0.8751 (mm) cc_final: 0.8524 (mp) REVERT: H 34 ASP cc_start: 0.6907 (m-30) cc_final: 0.6496 (t0) REVERT: H 179 GLN cc_start: 0.8994 (tt0) cc_final: 0.8704 (mt0) REVERT: H 181 TYR cc_start: 0.8458 (m-80) cc_final: 0.8209 (m-80) REVERT: I 240 ASN cc_start: 0.8166 (m-40) cc_final: 0.7917 (m-40) REVERT: J 143 MET cc_start: 0.8602 (mmt) cc_final: 0.8192 (mmt) REVERT: J 155 ASN cc_start: 0.7552 (t0) cc_final: 0.6971 (p0) REVERT: K 10 LEU cc_start: 0.8756 (mm) cc_final: 0.8527 (mp) REVERT: L 60 SER cc_start: 0.8846 (m) cc_final: 0.8486 (p) outliers start: 58 outliers final: 26 residues processed: 337 average time/residue: 0.1909 time to fit residues: 103.7084 Evaluate side-chains 280 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 246 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 298 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 338 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN C 132 HIS D 132 HIS ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 ASN I 132 HIS J 132 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.070722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062052 restraints weight = 97144.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.063876 restraints weight = 49894.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065125 restraints weight = 31443.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065971 restraints weight = 22383.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066551 restraints weight = 17367.289| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.347 29928 Z= 0.325 Angle : 0.792 17.387 40944 Z= 0.379 Chirality : 0.046 0.171 4392 Planarity : 0.006 0.060 5484 Dihedral : 9.384 86.551 4056 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.85 % Allowed : 15.21 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3684 helix: -0.79 (0.15), residues: 1116 sheet: -1.21 (0.19), residues: 828 loop : -0.57 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 238 TYR 0.020 0.002 TYR B 255 PHE 0.019 0.002 PHE K 243 TRP 0.020 0.002 TRP K 188 HIS 0.014 0.002 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00811 (29916) covalent geometry : angle 0.79155 (40944) hydrogen bonds : bond 0.03628 ( 1114) hydrogen bonds : angle 5.87730 ( 2874) Misc. bond : bond 0.18394 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 254 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 MET cc_start: 0.8763 (mmt) cc_final: 0.8474 (mmt) REVERT: D 105 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7811 (mm-30) REVERT: D 143 MET cc_start: 0.8563 (mmt) cc_final: 0.8214 (mmt) REVERT: D 155 ASN cc_start: 0.7697 (t0) cc_final: 0.7184 (p0) REVERT: E 182 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7501 (tt) REVERT: E 306 ASP cc_start: 0.8119 (t0) cc_final: 0.7299 (p0) REVERT: I 143 MET cc_start: 0.8760 (mmt) cc_final: 0.8472 (mmt) REVERT: J 105 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7815 (mm-30) REVERT: J 143 MET cc_start: 0.8562 (mmt) cc_final: 0.8213 (mmt) REVERT: J 155 ASN cc_start: 0.7693 (t0) cc_final: 0.7181 (p0) REVERT: K 182 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7435 (tt) REVERT: K 306 ASP cc_start: 0.8121 (t0) cc_final: 0.7306 (p0) outliers start: 88 outliers final: 53 residues processed: 330 average time/residue: 0.1814 time to fit residues: 98.8203 Evaluate side-chains 261 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 246 ILE Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 227 optimal weight: 7.9990 chunk 326 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 337 optimal weight: 0.0970 chunk 345 optimal weight: 4.9990 chunk 321 optimal weight: 0.0770 chunk 294 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS A 224 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065422 restraints weight = 94840.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067290 restraints weight = 47750.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068586 restraints weight = 29692.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069422 restraints weight = 20852.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070024 restraints weight = 16126.326| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29928 Z= 0.125 Angle : 0.621 7.730 40944 Z= 0.301 Chirality : 0.042 0.185 4392 Planarity : 0.005 0.043 5484 Dihedral : 9.144 85.439 4056 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.11 % Allowed : 16.34 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3684 helix: -0.19 (0.16), residues: 1104 sheet: -1.18 (0.19), residues: 792 loop : -0.37 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 238 TYR 0.017 0.001 TYR E 181 PHE 0.013 0.001 PHE H 251 TRP 0.008 0.001 TRP E 188 HIS 0.020 0.001 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00353 (29916) covalent geometry : angle 0.62059 (40944) hydrogen bonds : bond 0.02954 ( 1114) hydrogen bonds : angle 5.45662 ( 2874) Misc. bond : bond 0.04270 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: B 34 ASP cc_start: 0.7222 (m-30) cc_final: 0.6640 (t0) REVERT: B 112 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7916 (tm-30) REVERT: B 143 MET cc_start: 0.8226 (mmt) cc_final: 0.8006 (mmt) REVERT: B 250 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7314 (mp0) REVERT: C 143 MET cc_start: 0.8724 (mmt) cc_final: 0.8405 (mmt) REVERT: D 105 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 143 MET cc_start: 0.8651 (mmt) cc_final: 0.8290 (mmt) REVERT: D 155 ASN cc_start: 0.7662 (t0) cc_final: 0.7106 (p0) REVERT: E 182 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7366 (tt) REVERT: E 306 ASP cc_start: 0.8074 (t0) cc_final: 0.7308 (p0) REVERT: G 136 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: H 34 ASP cc_start: 0.7212 (m-30) cc_final: 0.6633 (t0) REVERT: H 112 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7914 (tm-30) REVERT: H 143 MET cc_start: 0.8223 (mmt) cc_final: 0.8000 (mmt) REVERT: H 250 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7318 (mp0) REVERT: I 143 MET cc_start: 0.8722 (mmt) cc_final: 0.8401 (mmt) REVERT: J 105 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7709 (mm-30) REVERT: J 143 MET cc_start: 0.8656 (mmt) cc_final: 0.8300 (mmt) REVERT: J 155 ASN cc_start: 0.7660 (t0) cc_final: 0.7106 (p0) REVERT: K 182 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7315 (tt) REVERT: K 306 ASP cc_start: 0.8078 (t0) cc_final: 0.7318 (p0) outliers start: 65 outliers final: 43 residues processed: 295 average time/residue: 0.1862 time to fit residues: 90.5351 Evaluate side-chains 253 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 121 MET Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 HIS ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.071561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.062979 restraints weight = 96238.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064808 restraints weight = 48966.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066073 restraints weight = 30699.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066905 restraints weight = 21695.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067494 restraints weight = 16818.766| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 29928 Z= 0.226 Angle : 0.676 8.380 40944 Z= 0.326 Chirality : 0.043 0.145 4392 Planarity : 0.005 0.050 5484 Dihedral : 9.082 85.409 4056 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.69 % Allowed : 16.31 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3684 helix: -0.16 (0.16), residues: 1104 sheet: -0.96 (0.19), residues: 828 loop : -0.37 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 74 TYR 0.025 0.002 TYR E 181 PHE 0.013 0.002 PHE G 296 TRP 0.008 0.001 TRP I 66 HIS 0.008 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00596 (29916) covalent geometry : angle 0.67627 (40944) hydrogen bonds : bond 0.03106 ( 1114) hydrogen bonds : angle 5.52523 ( 2874) Misc. bond : bond 0.11298 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8989 (tpt) cc_final: 0.8754 (tpp) REVERT: D 105 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7741 (mm-30) REVERT: D 143 MET cc_start: 0.8642 (mmt) cc_final: 0.8296 (mmt) REVERT: D 155 ASN cc_start: 0.7606 (t0) cc_final: 0.7112 (p0) REVERT: D 305 ASP cc_start: 0.7400 (m-30) cc_final: 0.6957 (t0) REVERT: E 182 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7916 (tt) REVERT: E 306 ASP cc_start: 0.8067 (t0) cc_final: 0.7317 (p0) REVERT: G 107 MET cc_start: 0.8986 (tpt) cc_final: 0.8755 (tpp) REVERT: J 105 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7740 (mm-30) REVERT: J 143 MET cc_start: 0.8642 (mmt) cc_final: 0.8303 (mmt) REVERT: J 155 ASN cc_start: 0.7614 (t0) cc_final: 0.7115 (p0) REVERT: J 305 ASP cc_start: 0.7410 (m-30) cc_final: 0.6964 (t0) REVERT: K 182 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7931 (tt) REVERT: K 306 ASP cc_start: 0.8068 (t0) cc_final: 0.7319 (p0) outliers start: 83 outliers final: 54 residues processed: 294 average time/residue: 0.1646 time to fit residues: 82.6936 Evaluate side-chains 258 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 341 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 328 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.069892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.061484 restraints weight = 97859.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063278 restraints weight = 49521.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064508 restraints weight = 30916.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.065276 restraints weight = 21862.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065843 restraints weight = 17149.487| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 29928 Z= 0.303 Angle : 0.745 10.553 40944 Z= 0.362 Chirality : 0.045 0.148 4392 Planarity : 0.006 0.057 5484 Dihedral : 9.200 85.017 4056 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.30 % Allowed : 17.35 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3684 helix: -0.30 (0.15), residues: 1104 sheet: -0.90 (0.19), residues: 828 loop : -0.53 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 49 TYR 0.041 0.002 TYR H 255 PHE 0.021 0.002 PHE A 296 TRP 0.010 0.002 TRP I 66 HIS 0.035 0.002 HIS G 177 Details of bonding type rmsd covalent geometry : bond 0.00769 (29916) covalent geometry : angle 0.74531 (40944) hydrogen bonds : bond 0.03433 ( 1114) hydrogen bonds : angle 5.72389 ( 2874) Misc. bond : bond 0.16976 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.9040 (tpt) cc_final: 0.8783 (tpp) REVERT: B 181 TYR cc_start: 0.8499 (m-80) cc_final: 0.8191 (m-10) REVERT: C 143 MET cc_start: 0.8748 (mmt) cc_final: 0.8483 (mmm) REVERT: D 105 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7697 (mm-30) REVERT: D 143 MET cc_start: 0.8712 (mmt) cc_final: 0.8354 (mmt) REVERT: D 305 ASP cc_start: 0.7347 (m-30) cc_final: 0.6968 (t0) REVERT: E 143 MET cc_start: 0.8815 (mmm) cc_final: 0.8495 (tmm) REVERT: E 182 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7983 (tt) REVERT: E 306 ASP cc_start: 0.8105 (t0) cc_final: 0.7387 (p0) REVERT: G 107 MET cc_start: 0.9037 (tpt) cc_final: 0.8783 (tpp) REVERT: H 181 TYR cc_start: 0.8494 (m-80) cc_final: 0.8184 (m-10) REVERT: I 143 MET cc_start: 0.8747 (mmt) cc_final: 0.8481 (mmm) REVERT: J 105 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7695 (mm-30) REVERT: J 143 MET cc_start: 0.8713 (mmt) cc_final: 0.8361 (mmt) REVERT: J 305 ASP cc_start: 0.7355 (m-30) cc_final: 0.6974 (t0) REVERT: K 143 MET cc_start: 0.8817 (mmm) cc_final: 0.8501 (tmm) REVERT: K 182 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7996 (tt) REVERT: K 306 ASP cc_start: 0.8107 (t0) cc_final: 0.7392 (p0) outliers start: 71 outliers final: 54 residues processed: 270 average time/residue: 0.1615 time to fit residues: 75.0391 Evaluate side-chains 248 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 246 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 262 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.062556 restraints weight = 96712.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064362 restraints weight = 49035.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065602 restraints weight = 30735.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066424 restraints weight = 21740.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.066987 restraints weight = 16797.349| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.187 29928 Z= 0.216 Angle : 0.674 9.360 40944 Z= 0.326 Chirality : 0.043 0.145 4392 Planarity : 0.005 0.045 5484 Dihedral : 9.128 85.554 4056 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.53 % Allowed : 17.51 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3684 helix: -0.07 (0.16), residues: 1032 sheet: -0.81 (0.19), residues: 828 loop : -0.46 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 238 TYR 0.043 0.002 TYR B 255 PHE 0.012 0.001 PHE G 296 TRP 0.007 0.001 TRP G 188 HIS 0.013 0.001 HIS L 183 Details of bonding type rmsd covalent geometry : bond 0.00570 (29916) covalent geometry : angle 0.67378 (40944) hydrogen bonds : bond 0.03161 ( 1114) hydrogen bonds : angle 5.55781 ( 2874) Misc. bond : bond 0.12499 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 211 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8384 (m-80) cc_final: 0.8089 (m-10) REVERT: C 143 MET cc_start: 0.8721 (mmt) cc_final: 0.8484 (mmm) REVERT: D 105 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 143 MET cc_start: 0.8720 (mmt) cc_final: 0.8322 (mmt) REVERT: D 305 ASP cc_start: 0.7364 (m-30) cc_final: 0.6915 (t0) REVERT: E 182 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8073 (tt) REVERT: E 306 ASP cc_start: 0.8044 (t0) cc_final: 0.7375 (p0) REVERT: G 107 MET cc_start: 0.8988 (tpt) cc_final: 0.8786 (tpp) REVERT: H 181 TYR cc_start: 0.8381 (m-80) cc_final: 0.8085 (m-10) REVERT: I 143 MET cc_start: 0.8719 (mmt) cc_final: 0.8479 (mmm) REVERT: J 105 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7688 (mm-30) REVERT: J 143 MET cc_start: 0.8720 (mmt) cc_final: 0.8326 (mmt) REVERT: J 305 ASP cc_start: 0.7372 (m-30) cc_final: 0.6920 (t0) REVERT: K 182 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8091 (tt) REVERT: K 306 ASP cc_start: 0.8047 (t0) cc_final: 0.7382 (p0) outliers start: 78 outliers final: 60 residues processed: 279 average time/residue: 0.1721 time to fit residues: 81.3924 Evaluate side-chains 258 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 196 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 121 MET Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 8 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 358 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 300 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 229 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 chunk 207 optimal weight: 0.0970 overall best weight: 2.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 224 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.071635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063211 restraints weight = 96518.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065047 restraints weight = 48785.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066296 restraints weight = 30300.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067122 restraints weight = 21308.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.067689 restraints weight = 16412.893| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 29928 Z= 0.178 Angle : 0.655 9.620 40944 Z= 0.316 Chirality : 0.043 0.146 4392 Planarity : 0.005 0.045 5484 Dihedral : 9.100 86.447 4056 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.20 % Allowed : 17.90 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3684 helix: 0.04 (0.17), residues: 1032 sheet: -0.72 (0.19), residues: 828 loop : -0.42 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 238 TYR 0.042 0.002 TYR B 255 PHE 0.017 0.001 PHE A 296 TRP 0.010 0.001 TRP E 188 HIS 0.013 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00483 (29916) covalent geometry : angle 0.65484 (40944) hydrogen bonds : bond 0.03079 ( 1114) hydrogen bonds : angle 5.49881 ( 2874) Misc. bond : bond 0.10001 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 216 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8433 (m-80) cc_final: 0.8138 (m-10) REVERT: C 143 MET cc_start: 0.8773 (mmt) cc_final: 0.8534 (mmm) REVERT: C 197 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7550 (mp0) REVERT: D 105 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7673 (mm-30) REVERT: D 143 MET cc_start: 0.8708 (mmt) cc_final: 0.8254 (mmt) REVERT: D 155 ASN cc_start: 0.7507 (t0) cc_final: 0.7027 (p0) REVERT: D 305 ASP cc_start: 0.7441 (m-30) cc_final: 0.6955 (t0) REVERT: E 68 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.8143 (ttp-170) REVERT: E 182 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8047 (tt) REVERT: E 306 ASP cc_start: 0.7977 (t0) cc_final: 0.7332 (p0) REVERT: H 181 TYR cc_start: 0.8434 (m-80) cc_final: 0.8140 (m-10) REVERT: I 143 MET cc_start: 0.8772 (mmt) cc_final: 0.8540 (mmm) REVERT: I 197 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7652 (mp0) REVERT: J 105 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7670 (mm-30) REVERT: J 143 MET cc_start: 0.8713 (mmt) cc_final: 0.8261 (mmt) REVERT: J 155 ASN cc_start: 0.7492 (t0) cc_final: 0.7021 (p0) REVERT: J 305 ASP cc_start: 0.7447 (m-30) cc_final: 0.6958 (t0) REVERT: K 68 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.8133 (ttp-170) REVERT: K 182 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8076 (tt) REVERT: K 306 ASP cc_start: 0.7980 (t0) cc_final: 0.7339 (p0) outliers start: 68 outliers final: 60 residues processed: 277 average time/residue: 0.1675 time to fit residues: 79.4095 Evaluate side-chains 265 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 203 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 183 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 343 optimal weight: 4.9990 chunk 334 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 314 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 287 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 319 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.063071 restraints weight = 96212.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064890 restraints weight = 48581.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066132 restraints weight = 30171.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066931 restraints weight = 21253.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067506 restraints weight = 16435.957| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 29928 Z= 0.196 Angle : 0.668 9.709 40944 Z= 0.323 Chirality : 0.043 0.200 4392 Planarity : 0.005 0.045 5484 Dihedral : 9.092 87.772 4056 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.24 % Allowed : 18.06 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.14), residues: 3684 helix: 0.04 (0.17), residues: 1032 sheet: -0.64 (0.19), residues: 828 loop : -0.38 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 238 TYR 0.025 0.002 TYR B 255 PHE 0.010 0.001 PHE G 19 TRP 0.010 0.001 TRP E 188 HIS 0.015 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00524 (29916) covalent geometry : angle 0.66807 (40944) hydrogen bonds : bond 0.03075 ( 1114) hydrogen bonds : angle 5.50553 ( 2874) Misc. bond : bond 0.10895 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 211 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 TYR cc_start: 0.8450 (m-80) cc_final: 0.8156 (m-10) REVERT: C 143 MET cc_start: 0.8773 (mmt) cc_final: 0.8536 (mmm) REVERT: C 197 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7570 (mp0) REVERT: D 105 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 143 MET cc_start: 0.8564 (mmt) cc_final: 0.8189 (mmt) REVERT: D 303 PHE cc_start: 0.8220 (t80) cc_final: 0.8013 (t80) REVERT: D 305 ASP cc_start: 0.7472 (m-30) cc_final: 0.6963 (t0) REVERT: E 143 MET cc_start: 0.8800 (tpt) cc_final: 0.8389 (tpp) REVERT: E 182 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8072 (tt) REVERT: E 306 ASP cc_start: 0.8020 (t0) cc_final: 0.7380 (p0) REVERT: H 181 TYR cc_start: 0.8450 (m-80) cc_final: 0.8156 (m-10) REVERT: I 143 MET cc_start: 0.8771 (mmt) cc_final: 0.8545 (mmm) REVERT: I 197 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7598 (mp0) REVERT: J 105 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7683 (mm-30) REVERT: J 143 MET cc_start: 0.8561 (mmt) cc_final: 0.8181 (mmt) REVERT: J 303 PHE cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: J 305 ASP cc_start: 0.7485 (m-30) cc_final: 0.6963 (t0) REVERT: K 143 MET cc_start: 0.8786 (tpt) cc_final: 0.8385 (tpp) REVERT: K 182 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8104 (tt) REVERT: K 306 ASP cc_start: 0.8024 (t0) cc_final: 0.7389 (p0) outliers start: 69 outliers final: 61 residues processed: 272 average time/residue: 0.1577 time to fit residues: 73.4591 Evaluate side-chains 268 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 289 THR Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 306 ASP Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 289 THR Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 302 ASP Chi-restraints excluded: chain L residue 306 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 106 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 257 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 HIS ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063046 restraints weight = 97483.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064878 restraints weight = 48993.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066123 restraints weight = 30331.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066955 restraints weight = 21283.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067520 restraints weight = 16347.717| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.171 29928 Z= 0.199 Angle : 0.666 9.530 40944 Z= 0.322 Chirality : 0.043 0.184 4392 Planarity : 0.005 0.045 5484 Dihedral : 9.098 89.176 4056 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.17 % Allowed : 18.39 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3684 helix: 0.04 (0.17), residues: 1032 sheet: -0.58 (0.19), residues: 828 loop : -0.38 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 238 TYR 0.021 0.002 TYR E 181 PHE 0.017 0.001 PHE G 296 TRP 0.008 0.001 TRP E 188 HIS 0.012 0.001 HIS F 183 Details of bonding type rmsd covalent geometry : bond 0.00528 (29916) covalent geometry : angle 0.66639 (40944) hydrogen bonds : bond 0.03081 ( 1114) hydrogen bonds : angle 5.52355 ( 2874) Misc. bond : bond 0.11031 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3956.04 seconds wall clock time: 69 minutes 51.18 seconds (4191.18 seconds total)