Starting phenix.real_space_refine on Sat Aug 10 11:10:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/08_2024/7bok_30131.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/08_2024/7bok_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/08_2024/7bok_30131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/08_2024/7bok_30131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/08_2024/7bok_30131.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bok_30131/08_2024/7bok_30131.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 267": "NH1" <-> "NH2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 267": "NH1" <-> "NH2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 267": "NH1" <-> "NH2" Residue "F PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 267": "NH1" <-> "NH2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 267": "NH1" <-> "NH2" Residue "I PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 267": "NH1" <-> "NH2" Residue "J PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 119": "OE1" <-> "OE2" Residue "K TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 267": "NH1" <-> "NH2" Residue "K PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 119": "OE1" <-> "OE2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 267": "NH1" <-> "NH2" Residue "L PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 15.13, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 10.91 Conformation dependent library (CDL) restraints added in 5.7 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: 3.86 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: 10.69 Time building geometry restraints manager: 11.95 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: 86.22 - 104.40: 862 104.40 - 122.58: 35632 122.58 - 140.76: 4426 140.76 - 158.94: 0 158.94 - 177.12: 24 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: 0.00 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 75.660 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.710 ------------------------------------------------------------------------------- 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 : 0.009 0.223 29916 Z= 0.589 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP H 66 HIS 0.004 0.001 HIS G 79 PHE 0.010 0.002 PHE C 303 TYR 0.009 0.002 TYR E 255 ARG 0.002 0.000 ARG I 238 *********************** 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 fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 3.494 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: 0.7041 (mt) REVERT: A 281 THR cc_start: 0.7158 (m) cc_final: 0.6713 (m) REVERT: B 240 ASN cc_start: 0.8572 (m-40) cc_final: 0.8344 (m-40) REVERT: C 13 LEU cc_start: 0.8536 (mt) cc_final: 0.8333 (tt) REVERT: C 139 ASN cc_start: 0.8480 (m-40) cc_final: 0.8157 (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: 0.7986 (mttt) REVERT: D 155 ASN cc_start: 0.7069 (t0) cc_final: 0.6865 (p0) REVERT: D 175 TYR cc_start: 0.8197 (m-80) cc_final: 0.7992 (m-80) REVERT: D 226 ILE cc_start: 0.8832 (mt) cc_final: 0.8569 (pt) REVERT: E 181 TYR cc_start: 0.8163 (m-80) cc_final: 0.7933 (m-80) REVERT: G 182 LEU cc_start: 0.8624 (mt) cc_final: 0.7037 (mt) REVERT: G 281 THR cc_start: 0.7152 (m) cc_final: 0.6705 (m) REVERT: H 240 ASN cc_start: 0.8573 (m-40) cc_final: 0.8346 (m-40) REVERT: I 139 ASN cc_start: 0.8481 (m-40) cc_final: 0.8157 (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: 0.7991 (mttt) REVERT: J 155 ASN cc_start: 0.7070 (t0) cc_final: 0.6866 (p0) REVERT: J 175 TYR cc_start: 0.8192 (m-80) cc_final: 0.7987 (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: 0.7937 (m-80) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.4427 time to fit residues: 440.4218 Evaluate side-chains 269 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS 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 183 HIS B 271 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 90 HIS 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 183 HIS H 271 ASN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 29916 Z= 0.388 Angle : 0.716 7.693 40944 Z= 0.358 Chirality : 0.044 0.172 4392 Planarity : 0.006 0.050 5484 Dihedral : 9.877 89.967 4056 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.04 % Allowed : 13.85 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 3684 helix: -1.82 (0.14), residues: 1056 sheet: -1.80 (0.19), residues: 828 loop : -0.82 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 188 HIS 0.009 0.001 HIS A 177 PHE 0.014 0.002 PHE J 145 TYR 0.014 0.002 TYR L 181 ARG 0.007 0.001 ARG C 267 *********************** 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 384 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 THR cc_start: 0.7140 (m) cc_final: 0.6769 (m) REVERT: B 46 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.8607 (tp) REVERT: B 185 MET cc_start: 0.8353 (mmp) cc_final: 0.8126 (mmp) REVERT: C 240 ASN cc_start: 0.8288 (m-40) cc_final: 0.8001 (m-40) REVERT: D 155 ASN cc_start: 0.7285 (t0) cc_final: 0.6824 (p0) REVERT: G 281 THR cc_start: 0.7141 (m) cc_final: 0.6768 (m) REVERT: H 46 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.8613 (tp) REVERT: H 185 MET cc_start: 0.8350 (mmp) cc_final: 0.8123 (mmp) REVERT: H 272 MET cc_start: 0.8435 (mtm) cc_final: 0.8232 (mtm) REVERT: I 240 ASN cc_start: 0.8308 (m-40) cc_final: 0.7991 (m-40) REVERT: J 155 ASN cc_start: 0.7285 (t0) cc_final: 0.6826 (p0) outliers start: 63 outliers final: 31 residues processed: 364 average time/residue: 0.4063 time to fit residues: 235.7679 Evaluate side-chains 279 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 3.269 ------------------------------------------------------------------------------- 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 206 ASP 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 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 206 ASP 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 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 181 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 132 HIS B 177 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** F 162 GLN ** 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 132 HIS 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 29916 Z= 0.361 Angle : 0.669 7.991 40944 Z= 0.328 Chirality : 0.043 0.173 4392 Planarity : 0.005 0.046 5484 Dihedral : 9.479 87.953 4056 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.50 % Allowed : 14.23 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3684 helix: -1.02 (0.15), residues: 1092 sheet: -1.50 (0.20), residues: 792 loop : -0.49 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 66 HIS 0.020 0.001 HIS F 183 PHE 0.011 0.001 PHE J 303 TYR 0.017 0.002 TYR K 181 ARG 0.004 0.001 ARG C 267 *********************** 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 351 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 274 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 ASP cc_start: 0.7078 (m-30) cc_final: 0.6640 (t0) REVERT: B 46 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8963 (mm) REVERT: C 143 MET cc_start: 0.8542 (mmm) cc_final: 0.7321 (mmm) REVERT: C 240 ASN cc_start: 0.8458 (m-40) cc_final: 0.8204 (m-40) REVERT: D 143 MET cc_start: 0.8591 (mmt) cc_final: 0.8203 (mmt) REVERT: D 155 ASN cc_start: 0.7377 (t0) cc_final: 0.6994 (p0) REVERT: E 189 ASN cc_start: 0.7972 (m-40) cc_final: 0.7709 (t0) REVERT: H 34 ASP cc_start: 0.7073 (m-30) cc_final: 0.6636 (t0) REVERT: H 46 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8968 (mm) REVERT: I 143 MET cc_start: 0.8546 (mmm) cc_final: 0.7311 (mmm) REVERT: I 240 ASN cc_start: 0.8466 (m-40) cc_final: 0.8210 (m-40) REVERT: J 143 MET cc_start: 0.8596 (mmt) cc_final: 0.8212 (mmt) REVERT: J 155 ASN cc_start: 0.7382 (t0) cc_final: 0.7000 (p0) REVERT: K 189 ASN cc_start: 0.7973 (m-40) cc_final: 0.7709 (t0) outliers start: 77 outliers final: 41 residues processed: 335 average time/residue: 0.3873 time to fit residues: 211.6161 Evaluate side-chains 269 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 2.913 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS 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 225 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 13 LEU 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 E residue 9 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain F residue 136 PHE 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 256 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS 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 225 VAL Chi-restraints excluded: chain I residue 256 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain J residue 13 LEU 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 K residue 9 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain L residue 136 PHE 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 323 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 D 132 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 ASN J 132 HIS ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 29916 Z= 0.420 Angle : 0.702 10.295 40944 Z= 0.343 Chirality : 0.044 0.155 4392 Planarity : 0.005 0.053 5484 Dihedral : 9.294 85.914 4056 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.24 % Allowed : 15.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3684 helix: -0.56 (0.15), residues: 1092 sheet: -1.23 (0.19), residues: 876 loop : -0.41 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 188 HIS 0.009 0.001 HIS F 183 PHE 0.015 0.002 PHE G 296 TYR 0.022 0.002 TYR H 255 ARG 0.005 0.001 ARG G 88 *********************** 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 366 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 266 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7778 (m-30) REVERT: A 107 MET cc_start: 0.9001 (tpt) cc_final: 0.8761 (tpp) REVERT: B 34 ASP cc_start: 0.7547 (m-30) cc_final: 0.7317 (m-30) REVERT: B 241 MET cc_start: 0.9112 (tpp) cc_final: 0.8564 (mmm) REVERT: C 143 MET cc_start: 0.8641 (mmm) cc_final: 0.7565 (mmm) REVERT: D 105 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7723 (mm-30) REVERT: D 143 MET cc_start: 0.8664 (mmt) cc_final: 0.8264 (mmt) REVERT: D 155 ASN cc_start: 0.7592 (t0) cc_final: 0.7107 (p0) REVERT: E 306 ASP cc_start: 0.8076 (t0) cc_final: 0.7315 (p0) REVERT: G 64 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: G 107 MET cc_start: 0.9006 (tpt) cc_final: 0.8765 (tpp) REVERT: H 34 ASP cc_start: 0.7543 (m-30) cc_final: 0.7317 (m-30) REVERT: H 241 MET cc_start: 0.9142 (tpp) cc_final: 0.8592 (mmm) REVERT: I 143 MET cc_start: 0.8650 (mmm) cc_final: 0.7569 (mmm) REVERT: J 105 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7724 (mm-30) REVERT: J 143 MET cc_start: 0.8666 (mmt) cc_final: 0.8267 (mmt) REVERT: J 155 ASN cc_start: 0.7594 (t0) cc_final: 0.7106 (p0) REVERT: K 306 ASP cc_start: 0.8076 (t0) cc_final: 0.7319 (p0) outliers start: 100 outliers final: 62 residues processed: 352 average time/residue: 0.3753 time to fit residues: 215.7632 Evaluate side-chains 280 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 216 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP 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 55 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS 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 109 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 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 13 LEU Chi-restraints excluded: chain D residue 36 LEU 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 109 VAL 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 38 ASP 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 256 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS 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 109 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 183 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 13 LEU Chi-restraints excluded: chain J residue 36 LEU 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 109 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.5980 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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** C 132 HIS ** D 224 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** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 ASN I 132 HIS ** J 224 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** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 29916 Z= 0.427 Angle : 0.692 9.264 40944 Z= 0.337 Chirality : 0.044 0.147 4392 Planarity : 0.005 0.050 5484 Dihedral : 9.254 85.297 4056 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.89 % Allowed : 16.05 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3684 helix: -0.45 (0.15), residues: 1104 sheet: -1.12 (0.19), residues: 876 loop : -0.39 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 188 HIS 0.016 0.001 HIS A 177 PHE 0.014 0.002 PHE C 251 TYR 0.014 0.002 TYR B 181 ARG 0.003 0.000 ARG C 267 *********************** 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 323 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 234 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: A 107 MET cc_start: 0.9017 (tpt) cc_final: 0.8508 (tpt) REVERT: A 112 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: B 143 MET cc_start: 0.8381 (mmt) cc_final: 0.7783 (mmm) REVERT: C 143 MET cc_start: 0.8650 (mmm) cc_final: 0.7728 (mmm) REVERT: C 155 ASN cc_start: 0.7292 (t0) cc_final: 0.7065 (t0) REVERT: D 105 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7739 (mm-30) REVERT: D 143 MET cc_start: 0.8674 (mmt) cc_final: 0.8262 (mmt) REVERT: D 305 ASP cc_start: 0.7417 (m-30) cc_final: 0.6967 (t0) REVERT: E 143 MET cc_start: 0.7789 (mmm) cc_final: 0.7426 (mmt) REVERT: E 306 ASP cc_start: 0.8098 (t0) cc_final: 0.7327 (p0) REVERT: G 64 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: G 107 MET cc_start: 0.9015 (tpt) cc_final: 0.8514 (tpt) REVERT: G 112 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: H 272 MET cc_start: 0.7913 (mtm) cc_final: 0.7605 (mtm) REVERT: I 143 MET cc_start: 0.8658 (mmm) cc_final: 0.7735 (mmm) REVERT: I 155 ASN cc_start: 0.7292 (t0) cc_final: 0.7067 (t0) REVERT: J 105 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7741 (mm-30) REVERT: J 143 MET cc_start: 0.8678 (mmt) cc_final: 0.8265 (mmt) REVERT: J 305 ASP cc_start: 0.7410 (m-30) cc_final: 0.6967 (t0) REVERT: K 143 MET cc_start: 0.7793 (mmm) cc_final: 0.7432 (mmt) REVERT: K 306 ASP cc_start: 0.8099 (t0) cc_final: 0.7333 (p0) outliers start: 89 outliers final: 69 residues processed: 305 average time/residue: 0.3678 time to fit residues: 185.9698 Evaluate side-chains 281 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 208 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 301 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 183 HIS 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 13 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 213 ASP 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 109 VAL 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 F residue 306 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 174 CYS Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 301 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 183 HIS 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 13 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 213 ASP 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 109 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 3.9990 chunk 313 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 348 optimal weight: 9.9990 chunk 289 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS G 224 ASN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 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** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29916 Z= 0.304 Angle : 0.637 8.739 40944 Z= 0.308 Chirality : 0.042 0.141 4392 Planarity : 0.005 0.044 5484 Dihedral : 9.097 84.305 4056 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.69 % Allowed : 17.06 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3684 helix: -0.14 (0.16), residues: 1104 sheet: -1.01 (0.19), residues: 876 loop : -0.30 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 188 HIS 0.008 0.001 HIS F 183 PHE 0.018 0.001 PHE C 251 TYR 0.016 0.001 TYR H 255 ARG 0.002 0.000 ARG J 202 *********************** 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 316 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 233 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: A 107 MET cc_start: 0.9008 (tpt) cc_final: 0.8804 (tpp) REVERT: A 112 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: B 143 MET cc_start: 0.8263 (mmt) cc_final: 0.7905 (mmm) REVERT: C 143 MET cc_start: 0.8640 (mmm) cc_final: 0.7713 (mmm) REVERT: C 155 ASN cc_start: 0.7251 (t0) cc_final: 0.7025 (t0) REVERT: D 105 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7710 (mm-30) REVERT: D 143 MET cc_start: 0.8646 (mmt) cc_final: 0.8254 (mmt) REVERT: D 155 ASN cc_start: 0.7799 (t0) cc_final: 0.7237 (p0) REVERT: D 305 ASP cc_start: 0.7446 (m-30) cc_final: 0.6976 (t0) REVERT: E 68 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8121 (ttp-170) REVERT: E 306 ASP cc_start: 0.8024 (t0) cc_final: 0.7319 (p0) REVERT: G 64 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: G 107 MET cc_start: 0.9013 (tpt) cc_final: 0.8806 (tpp) REVERT: H 143 MET cc_start: 0.8337 (mmt) cc_final: 0.7688 (mmm) REVERT: H 272 MET cc_start: 0.8036 (mtm) cc_final: 0.7677 (mtm) REVERT: I 143 MET cc_start: 0.8649 (mmm) cc_final: 0.7727 (mmm) REVERT: I 155 ASN cc_start: 0.7253 (t0) cc_final: 0.7024 (t0) REVERT: I 197 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7656 (mp0) REVERT: J 105 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7706 (mm-30) REVERT: J 143 MET cc_start: 0.8652 (mmt) cc_final: 0.8257 (mmt) REVERT: J 155 ASN cc_start: 0.7799 (t0) cc_final: 0.7237 (p0) REVERT: J 305 ASP cc_start: 0.7441 (m-30) cc_final: 0.6973 (t0) REVERT: K 68 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8117 (ttp-170) REVERT: K 306 ASP cc_start: 0.8027 (t0) cc_final: 0.7324 (p0) outliers start: 83 outliers final: 53 residues processed: 300 average time/residue: 0.3585 time to fit residues: 179.3478 Evaluate side-chains 272 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 216 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 112 GLU 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 128 VAL Chi-restraints excluded: chain B residue 174 CYS 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 128 VAL Chi-restraints excluded: chain C residue 183 HIS 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 130 GLU Chi-restraints excluded: chain D residue 136 PHE Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 213 ASP 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 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 302 ASP 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 256 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS 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 128 VAL Chi-restraints excluded: chain I residue 183 HIS 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 130 GLU Chi-restraints excluded: chain J residue 136 PHE Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 213 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 254 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 346 optimal weight: 9.9990 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS B 271 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** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 29916 Z= 0.404 Angle : 0.677 9.120 40944 Z= 0.328 Chirality : 0.043 0.165 4392 Planarity : 0.005 0.048 5484 Dihedral : 9.108 83.844 4056 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.24 % Allowed : 16.96 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3684 helix: -0.15 (0.16), residues: 1104 sheet: -0.96 (0.19), residues: 876 loop : -0.34 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 188 HIS 0.024 0.001 HIS A 177 PHE 0.019 0.002 PHE I 251 TYR 0.030 0.002 TYR H 255 ARG 0.003 0.000 ARG I 49 *********************** 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 321 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 221 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: A 107 MET cc_start: 0.8976 (tpt) cc_final: 0.8756 (tpp) REVERT: C 155 ASN cc_start: 0.7311 (t0) cc_final: 0.7105 (t0) REVERT: C 197 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7851 (mt-10) REVERT: D 105 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7716 (mm-30) REVERT: D 143 MET cc_start: 0.8673 (mmt) cc_final: 0.8280 (mmt) REVERT: D 155 ASN cc_start: 0.7948 (t0) cc_final: 0.7743 (t0) REVERT: D 305 ASP cc_start: 0.7438 (m-30) cc_final: 0.6914 (t0) REVERT: E 68 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8186 (ttp-170) REVERT: E 306 ASP cc_start: 0.8058 (t0) cc_final: 0.7370 (p0) REVERT: G 64 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: G 107 MET cc_start: 0.8978 (tpt) cc_final: 0.8755 (tpp) REVERT: H 272 MET cc_start: 0.8077 (mtm) cc_final: 0.7701 (mtm) REVERT: I 155 ASN cc_start: 0.7314 (t0) cc_final: 0.7107 (t0) REVERT: I 197 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7616 (mp0) REVERT: J 105 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7716 (mm-30) REVERT: J 143 MET cc_start: 0.8676 (mmt) cc_final: 0.8281 (mmt) REVERT: J 155 ASN cc_start: 0.7945 (t0) cc_final: 0.7740 (t0) REVERT: J 305 ASP cc_start: 0.7435 (m-30) cc_final: 0.6913 (t0) REVERT: K 68 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8184 (ttp-170) REVERT: K 306 ASP cc_start: 0.8060 (t0) cc_final: 0.7375 (p0) outliers start: 100 outliers final: 70 residues processed: 312 average time/residue: 0.3499 time to fit residues: 185.9222 Evaluate side-chains 274 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 202 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 174 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 301 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 183 HIS 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 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 109 VAL 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 306 ASP Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 136 PHE Chi-restraints excluded: chain G residue 174 CYS 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 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 301 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 183 HIS 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 I residue 300 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 109 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 0.1980 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 HIS F 218 ASN ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 HIS L 218 ASN ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29916 Z= 0.242 Angle : 0.619 9.261 40944 Z= 0.297 Chirality : 0.041 0.133 4392 Planarity : 0.005 0.043 5484 Dihedral : 8.993 83.440 4056 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.20 % Allowed : 18.13 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3684 helix: 0.10 (0.16), residues: 1104 sheet: -0.81 (0.19), residues: 864 loop : -0.20 (0.16), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 188 HIS 0.013 0.001 HIS F 183 PHE 0.018 0.001 PHE I 251 TYR 0.037 0.002 TYR H 255 ARG 0.003 0.000 ARG C 267 *********************** 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 310 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 242 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: C 143 MET cc_start: 0.8600 (mmm) cc_final: 0.7684 (mmm) REVERT: C 197 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7518 (mp0) REVERT: D 105 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 143 MET cc_start: 0.8674 (mmt) cc_final: 0.8249 (mmt) REVERT: D 155 ASN cc_start: 0.7850 (t0) cc_final: 0.7251 (p0) REVERT: D 305 ASP cc_start: 0.7495 (m-30) cc_final: 0.6987 (t0) REVERT: E 306 ASP cc_start: 0.7988 (t0) cc_final: 0.7345 (p0) REVERT: F 218 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7846 (p0) REVERT: G 64 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: I 143 MET cc_start: 0.8602 (mmm) cc_final: 0.7692 (mmm) REVERT: I 197 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7637 (mp0) REVERT: J 105 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7678 (mm-30) REVERT: J 143 MET cc_start: 0.8684 (mmt) cc_final: 0.8253 (mmt) REVERT: J 155 ASN cc_start: 0.7849 (t0) cc_final: 0.7249 (p0) REVERT: J 305 ASP cc_start: 0.7489 (m-30) cc_final: 0.6986 (t0) REVERT: K 306 ASP cc_start: 0.7990 (t0) cc_final: 0.7352 (p0) REVERT: L 218 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7840 (p0) outliers start: 68 outliers final: 50 residues processed: 302 average time/residue: 0.3704 time to fit residues: 185.2134 Evaluate side-chains 285 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 231 time to evaluate : 3.185 ------------------------------------------------------------------------------- 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 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU 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 F residue 85 ASP Chi-restraints excluded: chain F residue 136 PHE Chi-restraints excluded: chain F residue 218 ASN 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 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 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 183 HIS 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 256 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 136 PHE Chi-restraints excluded: chain L residue 218 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 6.9990 chunk 332 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 323 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 322 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** 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 177 HIS ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 177 HIS ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 29916 Z= 0.376 Angle : 0.677 9.111 40944 Z= 0.325 Chirality : 0.043 0.135 4392 Planarity : 0.005 0.046 5484 Dihedral : 9.030 83.927 4056 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.24 % Allowed : 18.51 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3684 helix: 0.02 (0.16), residues: 1104 sheet: -0.83 (0.19), residues: 876 loop : -0.28 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 66 HIS 0.011 0.001 HIS H 177 PHE 0.021 0.001 PHE C 251 TYR 0.038 0.002 TYR H 255 ARG 0.003 0.000 ARG J 238 *********************** 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 294 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 225 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: C 197 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7743 (mt-10) REVERT: D 105 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 305 ASP cc_start: 0.7543 (m-30) cc_final: 0.7015 (t0) REVERT: E 306 ASP cc_start: 0.8031 (t0) cc_final: 0.7378 (p0) REVERT: G 64 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: I 197 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7588 (mp0) REVERT: J 105 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7687 (mm-30) REVERT: J 155 ASN cc_start: 0.8019 (t0) cc_final: 0.7818 (t0) REVERT: J 305 ASP cc_start: 0.7540 (m-30) cc_final: 0.7014 (t0) REVERT: K 306 ASP cc_start: 0.8033 (t0) cc_final: 0.7384 (p0) outliers start: 69 outliers final: 61 residues processed: 284 average time/residue: 0.3474 time to fit residues: 166.0009 Evaluate side-chains 281 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 218 time to evaluate : 3.000 ------------------------------------------------------------------------------- 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 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 183 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 C residue 300 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 130 GLU 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 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 F residue 306 ASP 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 256 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 136 PHE Chi-restraints excluded: chain I residue 183 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 I residue 300 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 130 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 20.0000 chunk 341 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 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 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 HIS ** H 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 224 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 29916 Z= 0.427 Angle : 0.706 9.600 40944 Z= 0.340 Chirality : 0.044 0.141 4392 Planarity : 0.005 0.049 5484 Dihedral : 9.148 86.565 4056 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.20 % Allowed : 18.64 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3684 helix: -0.02 (0.16), residues: 1092 sheet: -0.63 (0.19), residues: 840 loop : -0.38 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 66 HIS 0.011 0.001 HIS L 183 PHE 0.028 0.002 PHE G 296 TYR 0.037 0.002 TYR H 255 ARG 0.003 0.000 ARG D 238 ********************** 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 281 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 213 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: B 241 MET cc_start: 0.8746 (mmm) cc_final: 0.8515 (tpp) REVERT: C 197 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7809 (mt-10) REVERT: D 105 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 143 MET cc_start: 0.8613 (mmt) cc_final: 0.8293 (mmt) REVERT: D 305 ASP cc_start: 0.7542 (m-30) cc_final: 0.6990 (t0) REVERT: E 143 MET cc_start: 0.7532 (mmm) cc_final: 0.6835 (tpp) REVERT: E 306 ASP cc_start: 0.8032 (t0) cc_final: 0.7382 (p0) REVERT: G 64 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: I 197 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7600 (mp0) REVERT: J 105 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7685 (mm-30) REVERT: J 143 MET cc_start: 0.8644 (mmt) cc_final: 0.8329 (mmt) REVERT: J 305 ASP cc_start: 0.7539 (m-30) cc_final: 0.6990 (t0) REVERT: K 143 MET cc_start: 0.7532 (mmm) cc_final: 0.6851 (tpp) REVERT: K 306 ASP cc_start: 0.8029 (t0) cc_final: 0.7386 (p0) outliers start: 68 outliers final: 62 residues processed: 279 average time/residue: 0.3659 time to fit residues: 170.6794 Evaluate side-chains 269 residues out of total 3084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP 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 174 CYS Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 301 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 183 HIS Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 300 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 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 F residue 306 ASP Chi-restraints excluded: chain G residue 64 ASP 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 174 CYS Chi-restraints excluded: chain H residue 206 ASP Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 301 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 183 HIS Chi-restraints excluded: chain I residue 274 ILE Chi-restraints excluded: chain I residue 281 THR Chi-restraints excluded: chain I residue 300 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 5.9990 chunk 304 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: