Starting phenix.real_space_refine on Tue Apr 16 05:08:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axl_15701/04_2024/8axl_15701.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axl_15701/04_2024/8axl_15701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axl_15701/04_2024/8axl_15701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axl_15701/04_2024/8axl_15701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axl_15701/04_2024/8axl_15701.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axl_15701/04_2024/8axl_15701.pdb" } resolution = 3.42 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 23805 2.51 5 N 6510 2.21 5 O 7275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 370": "NH1" <-> "NH2" Residue "O TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 462": "NH1" <-> "NH2" Residue "O PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 227": "NH1" <-> "NH2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 227": "NH1" <-> "NH2" Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 227": "NH1" <-> "NH2" Residue "E PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 462": "NH1" <-> "NH2" Residue "E PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 462": "NH1" <-> "NH2" Residue "F PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 227": "NH1" <-> "NH2" Residue "G PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 370": "NH1" <-> "NH2" Residue "G TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 462": "NH1" <-> "NH2" Residue "G PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 227": "NH1" <-> "NH2" Residue "H PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "H TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 462": "NH1" <-> "NH2" Residue "H PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 227": "NH1" <-> "NH2" Residue "I PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "I TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 462": "NH1" <-> "NH2" Residue "I PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 227": "NH1" <-> "NH2" Residue "J PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "J TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 462": "NH1" <-> "NH2" Residue "J PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 227": "NH1" <-> "NH2" Residue "K PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 370": "NH1" <-> "NH2" Residue "K TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 462": "NH1" <-> "NH2" Residue "K PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 227": "NH1" <-> "NH2" Residue "L PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 370": "NH1" <-> "NH2" Residue "L TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 462": "NH1" <-> "NH2" Residue "L PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 227": "NH1" <-> "NH2" Residue "M PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 370": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 462": "NH1" <-> "NH2" Residue "M PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 227": "NH1" <-> "NH2" Residue "N PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 370": "NH1" <-> "NH2" Residue "N TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 462": "NH1" <-> "NH2" Residue "N PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37650 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "O" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "F" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "G" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "H" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "I" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "J" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "K" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "L" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "M" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Chain: "N" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 11, 'TRANS': 308} Chain breaks: 4 Time building chain proxies: 19.41, per 1000 atoms: 0.52 Number of scatterers: 37650 At special positions: 0 Unit cell: (164.659, 163.275, 125.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 7275 8.00 N 6510 7.00 C 23805 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=0, symmetry=0 Time building additional restraints: 13.54 Conformation dependent library (CDL) restraints added in 6.9 seconds 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 19.1% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN A 497 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'O' and resid 209 through 218 Processing helix chain 'O' and resid 280 through 295 Processing helix chain 'O' and resid 418 through 420 No H-bonds generated for 'chain 'O' and resid 418 through 420' Processing helix chain 'O' and resid 444 through 449 Processing helix chain 'O' and resid 488 through 492 Processing helix chain 'O' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN O 497 " --> pdb=" O VAL O 494 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 525 removed outlier: 3.906A pdb=" N TYR O 525 " --> pdb=" O GLU O 522 " (cutoff:3.500A) Processing helix chain 'O' and resid 536 through 545 Processing helix chain 'B' and resid 209 through 218 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN B 497 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'C' and resid 209 through 218 Processing helix chain 'C' and resid 280 through 295 Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN C 497 " --> pdb=" O VAL C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'D' and resid 209 through 218 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN D 497 " --> pdb=" O VAL D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR D 525 " --> pdb=" O GLU D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 418 through 420 No H-bonds generated for 'chain 'E' and resid 418 through 420' Processing helix chain 'E' and resid 444 through 449 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN E 497 " --> pdb=" O VAL E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR E 525 " --> pdb=" O GLU E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 545 Processing helix chain 'F' and resid 209 through 218 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 444 through 449 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN F 497 " --> pdb=" O VAL F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR F 525 " --> pdb=" O GLU F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 545 Processing helix chain 'G' and resid 209 through 218 Processing helix chain 'G' and resid 280 through 295 Processing helix chain 'G' and resid 418 through 420 No H-bonds generated for 'chain 'G' and resid 418 through 420' Processing helix chain 'G' and resid 444 through 449 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN G 497 " --> pdb=" O VAL G 494 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR G 525 " --> pdb=" O GLU G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 545 Processing helix chain 'H' and resid 209 through 218 Processing helix chain 'H' and resid 280 through 295 Processing helix chain 'H' and resid 418 through 420 No H-bonds generated for 'chain 'H' and resid 418 through 420' Processing helix chain 'H' and resid 444 through 449 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN H 497 " --> pdb=" O VAL H 494 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 525 removed outlier: 3.906A pdb=" N TYR H 525 " --> pdb=" O GLU H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 545 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 280 through 295 Processing helix chain 'I' and resid 418 through 420 No H-bonds generated for 'chain 'I' and resid 418 through 420' Processing helix chain 'I' and resid 444 through 449 Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN I 497 " --> pdb=" O VAL I 494 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR I 525 " --> pdb=" O GLU I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 545 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 280 through 295 Processing helix chain 'J' and resid 418 through 420 No H-bonds generated for 'chain 'J' and resid 418 through 420' Processing helix chain 'J' and resid 444 through 449 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN J 497 " --> pdb=" O VAL J 494 " (cutoff:3.500A) Processing helix chain 'J' and resid 521 through 525 removed outlier: 3.906A pdb=" N TYR J 525 " --> pdb=" O GLU J 522 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 545 Processing helix chain 'K' and resid 209 through 218 Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 418 through 420 No H-bonds generated for 'chain 'K' and resid 418 through 420' Processing helix chain 'K' and resid 444 through 449 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN K 497 " --> pdb=" O VAL K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR K 525 " --> pdb=" O GLU K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 536 through 545 Processing helix chain 'L' and resid 209 through 218 Processing helix chain 'L' and resid 280 through 295 Processing helix chain 'L' and resid 418 through 420 No H-bonds generated for 'chain 'L' and resid 418 through 420' Processing helix chain 'L' and resid 444 through 449 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 494 through 499 removed outlier: 3.877A pdb=" N ASN L 497 " --> pdb=" O VAL L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR L 525 " --> pdb=" O GLU L 522 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 545 Processing helix chain 'M' and resid 209 through 218 Processing helix chain 'M' and resid 280 through 295 Processing helix chain 'M' and resid 418 through 420 No H-bonds generated for 'chain 'M' and resid 418 through 420' Processing helix chain 'M' and resid 444 through 449 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN M 497 " --> pdb=" O VAL M 494 " (cutoff:3.500A) Processing helix chain 'M' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR M 525 " --> pdb=" O GLU M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 536 through 545 Processing helix chain 'N' and resid 209 through 218 Processing helix chain 'N' and resid 280 through 295 Processing helix chain 'N' and resid 418 through 420 No H-bonds generated for 'chain 'N' and resid 418 through 420' Processing helix chain 'N' and resid 444 through 449 Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 494 through 499 removed outlier: 3.878A pdb=" N ASN N 497 " --> pdb=" O VAL N 494 " (cutoff:3.500A) Processing helix chain 'N' and resid 521 through 525 removed outlier: 3.907A pdb=" N TYR N 525 " --> pdb=" O GLU N 522 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 198 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.154A pdb=" N ARG A 227 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL B 185 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 229 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LYS B 187 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 332 through 336 current: chain 'A' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 501 through 519 current: chain 'O' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 332 through 336 current: chain 'O' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 501 through 519 current: chain 'B' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 332 through 336 current: chain 'B' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 501 through 519 current: chain 'C' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 332 through 336 current: chain 'C' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 501 through 519 current: chain 'D' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 332 through 336 current: chain 'D' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 501 through 519 current: chain 'E' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 332 through 336 current: chain 'E' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 501 through 519 current: chain 'F' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 332 through 336 current: chain 'F' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 501 through 519 current: chain 'G' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 332 through 336 current: chain 'G' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 501 through 519 current: chain 'H' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 332 through 336 current: chain 'H' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 501 through 519 current: chain 'I' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 332 through 336 current: chain 'I' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 501 through 519 current: chain 'J' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 332 through 336 current: chain 'J' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 501 through 519 current: chain 'K' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 332 through 336 current: chain 'K' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 501 through 519 current: chain 'L' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 332 through 336 current: chain 'L' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 501 through 519 current: chain 'M' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 332 through 336 current: chain 'M' and resid 501 through 519 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 501 through 519 current: chain 'N' and resid 332 through 336 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 332 through 336 current: chain 'N' and resid 501 through 519 Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 391 Processing sheet with id=AA6, first strand: chain 'O' and resid 265 through 269 Processing sheet with id=AA7, first strand: chain 'O' and resid 196 through 198 Processing sheet with id=AA8, first strand: chain 'B' and resid 196 through 198 Processing sheet with id=AA9, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.197A pdb=" N ARG B 227 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL C 185 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 229 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS C 187 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 196 through 198 Processing sheet with id=AB2, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG C 227 " --> pdb=" O PHE D 183 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL D 185 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA C 229 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS D 187 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 196 through 198 Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG D 227 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL E 185 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA D 229 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYS E 187 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 196 through 198 Processing sheet with id=AB6, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG E 227 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL F 185 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA E 229 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS F 187 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 196 through 198 Processing sheet with id=AB8, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.208A pdb=" N ARG F 227 " --> pdb=" O PHE G 183 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL G 185 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA F 229 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LYS G 187 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 196 through 198 Processing sheet with id=AC1, first strand: chain 'G' and resid 226 through 229 removed outlier: 6.235A pdb=" N ARG G 227 " --> pdb=" O PHE H 183 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N VAL H 185 " --> pdb=" O ARG G 227 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA G 229 " --> pdb=" O VAL H 185 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N LYS H 187 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 196 through 198 Processing sheet with id=AC3, first strand: chain 'H' and resid 226 through 229 removed outlier: 6.269A pdb=" N ARG H 227 " --> pdb=" O PHE I 183 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL I 185 " --> pdb=" O ARG H 227 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA H 229 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LYS I 187 " --> pdb=" O ALA H 229 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 196 through 198 Processing sheet with id=AC5, first strand: chain 'I' and resid 226 through 229 Processing sheet with id=AC6, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC7, first strand: chain 'J' and resid 226 through 229 removed outlier: 6.115A pdb=" N ARG J 227 " --> pdb=" O PHE K 183 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N VAL K 185 " --> pdb=" O ARG J 227 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA J 229 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LYS K 187 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 196 through 198 Processing sheet with id=AC9, first strand: chain 'K' and resid 226 through 229 removed outlier: 6.187A pdb=" N ARG K 227 " --> pdb=" O PHE L 183 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL L 185 " --> pdb=" O ARG K 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA K 229 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS L 187 " --> pdb=" O ALA K 229 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 196 through 198 Processing sheet with id=AD2, first strand: chain 'L' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG L 227 " --> pdb=" O PHE M 183 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL M 185 " --> pdb=" O ARG L 227 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA L 229 " --> pdb=" O VAL M 185 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS M 187 " --> pdb=" O ALA L 229 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AD4, first strand: chain 'M' and resid 226 through 229 removed outlier: 6.188A pdb=" N ARG M 227 " --> pdb=" O PHE N 183 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL N 185 " --> pdb=" O ARG M 227 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA M 229 " --> pdb=" O VAL N 185 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS N 187 " --> pdb=" O ALA M 229 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 196 through 198 1323 hydrogen bonds defined for protein. 3381 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: 14.81 Time building geometry restraints manager: 14.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12438 1.34 - 1.46: 6110 1.46 - 1.57: 19492 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 38160 Sorted by residual: bond pdb=" CA ARG M 511 " pdb=" CB ARG M 511 " ideal model delta sigma weight residual 1.535 1.512 0.023 2.02e-02 2.45e+03 1.31e+00 bond pdb=" CB ASN M 411 " pdb=" CG ASN M 411 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CB ASN E 411 " pdb=" CG ASN E 411 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CA ARG O 511 " pdb=" CB ARG O 511 " ideal model delta sigma weight residual 1.535 1.512 0.023 2.02e-02 2.45e+03 1.31e+00 bond pdb=" CB ASN I 411 " pdb=" CG ASN I 411 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.30e+00 ... (remaining 38155 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.48: 795 106.48 - 113.35: 22186 113.35 - 120.22: 12418 120.22 - 127.08: 15991 127.08 - 133.95: 225 Bond angle restraints: 51615 Sorted by residual: angle pdb=" C VAL C 296 " pdb=" N ALA C 297 " pdb=" CA ALA C 297 " ideal model delta sigma weight residual 122.15 115.02 7.13 2.83e+00 1.25e-01 6.34e+00 angle pdb=" C VAL I 296 " pdb=" N ALA I 297 " pdb=" CA ALA I 297 " ideal model delta sigma weight residual 122.15 115.03 7.12 2.83e+00 1.25e-01 6.33e+00 angle pdb=" C VAL A 296 " pdb=" N ALA A 297 " pdb=" CA ALA A 297 " ideal model delta sigma weight residual 122.15 115.04 7.11 2.83e+00 1.25e-01 6.32e+00 angle pdb=" C VAL G 296 " pdb=" N ALA G 297 " pdb=" CA ALA G 297 " ideal model delta sigma weight residual 122.15 115.04 7.11 2.83e+00 1.25e-01 6.31e+00 angle pdb=" C VAL J 296 " pdb=" N ALA J 297 " pdb=" CA ALA J 297 " ideal model delta sigma weight residual 122.15 115.05 7.10 2.83e+00 1.25e-01 6.30e+00 ... (remaining 51610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 20490 11.91 - 23.82: 1800 23.82 - 35.73: 765 35.73 - 47.64: 165 47.64 - 59.55: 75 Dihedral angle restraints: 23295 sinusoidal: 9405 harmonic: 13890 Sorted by residual: dihedral pdb=" CA LYS K 351 " pdb=" C LYS K 351 " pdb=" N PHE K 352 " pdb=" CA PHE K 352 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LYS N 351 " pdb=" C LYS N 351 " pdb=" N PHE N 352 " pdb=" CA PHE N 352 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA LYS M 351 " pdb=" C LYS M 351 " pdb=" N PHE M 352 " pdb=" CA PHE M 352 " ideal model delta harmonic sigma weight residual -180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 23292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3237 0.028 - 0.056: 1826 0.056 - 0.083: 409 0.083 - 0.111: 397 0.111 - 0.139: 281 Chirality restraints: 6150 Sorted by residual: chirality pdb=" CA PRO I 487 " pdb=" N PRO I 487 " pdb=" C PRO I 487 " pdb=" CB PRO I 487 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO A 487 " pdb=" N PRO A 487 " pdb=" C PRO A 487 " pdb=" CB PRO A 487 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE M 486 " pdb=" N ILE M 486 " pdb=" C ILE M 486 " pdb=" CB ILE M 486 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 6147 not shown) Planarity restraints: 6600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 370 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO L 371 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO L 371 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 371 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 370 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO N 371 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO N 371 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO N 371 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 370 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO K 371 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO K 371 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 371 " 0.031 5.00e-02 4.00e+02 ... (remaining 6597 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2428 2.73 - 3.27: 36875 3.27 - 3.81: 56951 3.81 - 4.36: 67229 4.36 - 4.90: 124611 Nonbonded interactions: 288094 Sorted by model distance: nonbonded pdb=" NZ LYS I 298 " pdb=" O GLU J 271 " model vdw 2.183 2.520 nonbonded pdb=" OH TYR A 531 " pdb=" OG SER O 304 " model vdw 2.193 2.440 nonbonded pdb=" OG SER I 304 " pdb=" OH TYR J 531 " model vdw 2.197 2.440 nonbonded pdb=" OG SER H 304 " pdb=" OH TYR I 531 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR O 531 " pdb=" OG SER N 304 " model vdw 2.199 2.440 ... (remaining 288089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 23.250 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 95.610 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.006 0.031 38160 Z= 0.415 Angle : 0.646 7.128 51615 Z= 0.371 Chirality : 0.047 0.139 6150 Planarity : 0.005 0.057 6600 Dihedral : 11.799 59.548 14265 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.47 % Allowed : 8.33 % Favored : 88.19 % 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: -0.64 (0.12), residues: 4650 helix: -0.36 (0.20), residues: 705 sheet: 0.48 (0.10), residues: 2640 loop : -2.30 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 306 HIS 0.004 0.002 HIS H 300 PHE 0.013 0.001 PHE M 513 TYR 0.010 0.001 TYR E 474 ARG 0.003 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 696 time to evaluate : 4.695 Fit side-chains REVERT: A 362 LYS cc_start: 0.8205 (mttt) cc_final: 0.7988 (mtmm) REVERT: A 408 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8656 (t) REVERT: O 228 GLN cc_start: 0.7033 (mt0) cc_final: 0.6676 (mt0) REVERT: O 289 ASP cc_start: 0.7560 (m-30) cc_final: 0.6834 (m-30) REVERT: O 405 THR cc_start: 0.8878 (m) cc_final: 0.8640 (t) REVERT: O 501 TYR cc_start: 0.8521 (t80) cc_final: 0.7913 (t80) REVERT: B 280 ASN cc_start: 0.7496 (m-40) cc_final: 0.7193 (m110) REVERT: B 362 LYS cc_start: 0.8141 (mttt) cc_final: 0.7887 (mtpt) REVERT: C 266 LEU cc_start: 0.8619 (tt) cc_final: 0.8332 (tt) REVERT: C 362 LYS cc_start: 0.8211 (mttt) cc_final: 0.7936 (mtmm) REVERT: C 405 THR cc_start: 0.8915 (m) cc_final: 0.8651 (t) REVERT: D 215 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7725 (tm-30) REVERT: D 266 LEU cc_start: 0.8641 (tt) cc_final: 0.8402 (tt) REVERT: D 405 THR cc_start: 0.8863 (m) cc_final: 0.8644 (t) REVERT: E 266 LEU cc_start: 0.8752 (tt) cc_final: 0.8412 (tt) REVERT: E 280 ASN cc_start: 0.7725 (m-40) cc_final: 0.7054 (m110) REVERT: E 405 THR cc_start: 0.8909 (m) cc_final: 0.8643 (t) REVERT: F 266 LEU cc_start: 0.8694 (tt) cc_final: 0.8294 (tt) REVERT: F 280 ASN cc_start: 0.7724 (m-40) cc_final: 0.7434 (m110) REVERT: F 303 LEU cc_start: 0.8984 (tp) cc_final: 0.8564 (tp) REVERT: F 405 THR cc_start: 0.8899 (m) cc_final: 0.8683 (t) REVERT: F 424 MET cc_start: 0.7552 (mtm) cc_final: 0.7244 (mtm) REVERT: G 266 LEU cc_start: 0.8389 (tt) cc_final: 0.7970 (tt) REVERT: G 269 TYR cc_start: 0.8564 (t80) cc_final: 0.8138 (t80) REVERT: G 362 LYS cc_start: 0.8253 (mttt) cc_final: 0.7988 (mttt) REVERT: G 526 TYR cc_start: 0.9152 (m-80) cc_final: 0.8899 (m-80) REVERT: G 539 GLU cc_start: 0.7862 (tp30) cc_final: 0.7591 (tp30) REVERT: H 266 LEU cc_start: 0.8591 (tt) cc_final: 0.8365 (tt) REVERT: H 280 ASN cc_start: 0.7482 (m-40) cc_final: 0.7242 (m110) REVERT: H 289 ASP cc_start: 0.7436 (m-30) cc_final: 0.6848 (m-30) REVERT: H 394 VAL cc_start: 0.7806 (m) cc_final: 0.7451 (p) REVERT: H 411 ASN cc_start: 0.8666 (p0) cc_final: 0.8036 (p0) REVERT: H 429 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7095 (mt-10) REVERT: H 471 ILE cc_start: 0.9459 (pt) cc_final: 0.9217 (pt) REVERT: I 195 ASP cc_start: 0.7993 (m-30) cc_final: 0.7712 (p0) REVERT: I 266 LEU cc_start: 0.8417 (tt) cc_final: 0.8203 (tt) REVERT: I 280 ASN cc_start: 0.7586 (m-40) cc_final: 0.7206 (m110) REVERT: I 289 ASP cc_start: 0.7437 (m-30) cc_final: 0.6894 (m-30) REVERT: I 332 PHE cc_start: 0.7989 (t80) cc_final: 0.7776 (t80) REVERT: I 357 MET cc_start: 0.6931 (tpp) cc_final: 0.6373 (mpp) REVERT: J 194 SER cc_start: 0.9108 (m) cc_final: 0.8396 (p) REVERT: J 195 ASP cc_start: 0.8159 (m-30) cc_final: 0.7901 (p0) REVERT: J 408 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8594 (p) REVERT: J 451 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7626 (mt-10) REVERT: K 181 VAL cc_start: 0.7219 (t) cc_final: 0.7014 (p) REVERT: K 302 GLU cc_start: 0.8111 (tt0) cc_final: 0.7858 (tt0) REVERT: K 338 MET cc_start: 0.7628 (mmm) cc_final: 0.7329 (mmm) REVERT: K 362 LYS cc_start: 0.8127 (mttt) cc_final: 0.7828 (mttt) REVERT: K 405 THR cc_start: 0.8732 (m) cc_final: 0.8463 (t) REVERT: K 410 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8887 (pt) REVERT: K 526 TYR cc_start: 0.9225 (m-80) cc_final: 0.8931 (m-80) REVERT: K 539 GLU cc_start: 0.7915 (tp30) cc_final: 0.7417 (tp30) REVERT: L 405 THR cc_start: 0.8910 (m) cc_final: 0.8664 (t) REVERT: M 266 LEU cc_start: 0.8826 (tt) cc_final: 0.8579 (tt) REVERT: M 282 GLN cc_start: 0.7417 (mt0) cc_final: 0.7207 (mt0) REVERT: M 286 ILE cc_start: 0.8306 (pt) cc_final: 0.7990 (pt) REVERT: M 289 ASP cc_start: 0.7322 (m-30) cc_final: 0.6817 (m-30) REVERT: M 303 LEU cc_start: 0.8987 (tp) cc_final: 0.8718 (tp) REVERT: M 539 GLU cc_start: 0.7772 (tp30) cc_final: 0.7505 (tp30) REVERT: N 405 THR cc_start: 0.8887 (m) cc_final: 0.8660 (t) REVERT: N 539 GLU cc_start: 0.7925 (tp30) cc_final: 0.7696 (tp30) outliers start: 150 outliers final: 70 residues processed: 817 average time/residue: 0.4941 time to fit residues: 658.0922 Evaluate side-chains 585 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 512 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain O residue 514 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain H residue 514 LEU Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 514 LEU Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain M residue 514 LEU Chi-restraints excluded: chain N residue 356 VAL Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 0.8980 chunk 363 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 376 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 280 optimal weight: 0.9980 chunk 435 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN C 361 GLN D 361 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 ASN E 361 GLN G 280 ASN G 361 GLN ** H 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 GLN L 361 GLN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN N 361 GLN N 376 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 38160 Z= 0.273 Angle : 0.575 6.784 51615 Z= 0.308 Chirality : 0.048 0.172 6150 Planarity : 0.004 0.051 6600 Dihedral : 7.456 59.933 5211 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.31 % Allowed : 12.48 % Favored : 83.22 % 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 (0.12), residues: 4650 helix: -0.37 (0.20), residues: 705 sheet: 0.62 (0.10), residues: 2640 loop : -2.31 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 306 HIS 0.005 0.002 HIS A 300 PHE 0.016 0.001 PHE N 332 TYR 0.015 0.001 TYR H 501 ARG 0.006 0.000 ARG N 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 596 time to evaluate : 4.516 Fit side-chains revert: symmetry clash REVERT: A 195 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7783 (p0) REVERT: O 195 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: O 228 GLN cc_start: 0.6840 (mt0) cc_final: 0.6553 (mt0) REVERT: O 289 ASP cc_start: 0.7421 (m-30) cc_final: 0.6718 (m-30) REVERT: O 405 THR cc_start: 0.8831 (m) cc_final: 0.8623 (t) REVERT: B 195 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: B 280 ASN cc_start: 0.7552 (m-40) cc_final: 0.7264 (m110) REVERT: B 362 LYS cc_start: 0.8272 (mttt) cc_final: 0.8024 (mtpt) REVERT: C 195 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7939 (p0) REVERT: C 266 LEU cc_start: 0.8555 (tt) cc_final: 0.8285 (tt) REVERT: C 357 MET cc_start: 0.6820 (tpp) cc_final: 0.6384 (mtt) REVERT: D 195 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7580 (p0) REVERT: D 215 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 227 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5854 (mmt-90) REVERT: D 405 THR cc_start: 0.8810 (m) cc_final: 0.8605 (t) REVERT: E 266 LEU cc_start: 0.8772 (tt) cc_final: 0.8528 (tt) REVERT: E 280 ASN cc_start: 0.7548 (m-40) cc_final: 0.6978 (m110) REVERT: E 405 THR cc_start: 0.8860 (m) cc_final: 0.8611 (t) REVERT: F 195 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7813 (p0) REVERT: F 200 MET cc_start: 0.8773 (mmp) cc_final: 0.8486 (mmp) REVERT: F 227 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.5384 (mmt-90) REVERT: F 266 LEU cc_start: 0.8670 (tt) cc_final: 0.8240 (tt) REVERT: F 280 ASN cc_start: 0.7669 (m-40) cc_final: 0.7384 (m110) REVERT: F 303 LEU cc_start: 0.9208 (tp) cc_final: 0.8834 (tp) REVERT: F 405 THR cc_start: 0.8821 (m) cc_final: 0.8617 (t) REVERT: F 424 MET cc_start: 0.7869 (mtm) cc_final: 0.7667 (mtp) REVERT: G 195 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7920 (p0) REVERT: G 266 LEU cc_start: 0.8547 (tt) cc_final: 0.8176 (tt) REVERT: G 362 LYS cc_start: 0.8454 (mttt) cc_final: 0.8173 (mttt) REVERT: G 526 TYR cc_start: 0.9226 (m-80) cc_final: 0.8829 (m-80) REVERT: G 539 GLU cc_start: 0.7811 (tp30) cc_final: 0.7568 (tp30) REVERT: H 195 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7765 (p0) REVERT: H 266 LEU cc_start: 0.8631 (tt) cc_final: 0.8361 (tt) REVERT: H 411 ASN cc_start: 0.8491 (p0) cc_final: 0.7885 (p0) REVERT: H 429 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7053 (mt-10) REVERT: I 195 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7778 (p0) REVERT: I 266 LEU cc_start: 0.8458 (tt) cc_final: 0.8191 (tt) REVERT: I 280 ASN cc_start: 0.7537 (m-40) cc_final: 0.7184 (m110) REVERT: I 289 ASP cc_start: 0.7439 (m-30) cc_final: 0.6950 (m-30) REVERT: I 332 PHE cc_start: 0.8189 (t80) cc_final: 0.7988 (t80) REVERT: J 194 SER cc_start: 0.9220 (m) cc_final: 0.8223 (p) REVERT: J 195 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7933 (p0) REVERT: K 195 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: K 227 ARG cc_start: 0.6704 (OUTLIER) cc_final: 0.6439 (mmt180) REVERT: K 303 LEU cc_start: 0.9043 (tp) cc_final: 0.8732 (tp) REVERT: K 362 LYS cc_start: 0.8391 (mttt) cc_final: 0.8176 (mttt) REVERT: K 410 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8896 (pt) REVERT: K 411 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8184 (p0) REVERT: K 455 THR cc_start: 0.8450 (m) cc_final: 0.8200 (m) REVERT: K 526 TYR cc_start: 0.9208 (m-80) cc_final: 0.8894 (m-80) REVERT: L 195 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7829 (p0) REVERT: L 227 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.5906 (mmt-90) REVERT: L 338 MET cc_start: 0.8020 (mmm) cc_final: 0.7610 (mmm) REVERT: M 266 LEU cc_start: 0.8892 (tt) cc_final: 0.8631 (tt) REVERT: N 195 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7911 (p0) REVERT: N 227 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.5895 (mmt-90) REVERT: N 377 GLU cc_start: 0.8405 (pt0) cc_final: 0.8038 (pt0) REVERT: N 539 GLU cc_start: 0.7890 (tp30) cc_final: 0.7599 (tp30) outliers start: 186 outliers final: 134 residues processed: 720 average time/residue: 0.5020 time to fit residues: 586.5701 Evaluate side-chains 668 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 514 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 195 ASP Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 353 ILE Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 195 ASP Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 317 ASN Chi-restraints excluded: chain I residue 404 VAL Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain J residue 408 THR Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 411 ASN Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 195 ASP Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 317 ASN Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 362 LYS Chi-restraints excluded: chain M residue 401 LEU Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 411 ASN Chi-restraints excluded: chain M residue 424 MET Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain N residue 195 ASP Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 chunk 296 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 436 optimal weight: 0.7980 chunk 471 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 433 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 350 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** O 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 376 GLN B 465 GLN B 476 HIS C 376 GLN C 465 GLN D 476 HIS E 376 GLN E 476 HIS F 361 GLN F 376 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 HIS ** G 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 476 HIS ** I 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 361 GLN J 476 HIS K 376 GLN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 GLN N 476 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 38160 Z= 0.410 Angle : 0.633 7.434 51615 Z= 0.338 Chirality : 0.049 0.168 6150 Planarity : 0.005 0.056 6600 Dihedral : 7.298 59.601 5191 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.67 % Allowed : 13.87 % Favored : 79.47 % 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: -0.59 (0.13), residues: 4650 helix: -0.47 (0.20), residues: 705 sheet: 0.53 (0.10), residues: 2670 loop : -2.28 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 306 HIS 0.007 0.002 HIS I 300 PHE 0.018 0.002 PHE G 328 TYR 0.014 0.002 TYR F 501 ARG 0.007 0.001 ARG B 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9300 Ramachandran restraints generated. 4650 Oldfield, 0 Emsley, 4650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 537 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7773 (p0) REVERT: A 289 ASP cc_start: 0.7776 (t0) cc_final: 0.7305 (t0) REVERT: O 228 GLN cc_start: 0.6855 (mt0) cc_final: 0.6568 (mt0) REVERT: O 289 ASP cc_start: 0.7332 (m-30) cc_final: 0.6851 (m-30) REVERT: O 405 THR cc_start: 0.8874 (m) cc_final: 0.8669 (t) REVERT: B 266 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8217 (tt) REVERT: B 280 ASN cc_start: 0.7553 (m-40) cc_final: 0.7266 (m110) REVERT: C 227 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5566 (mmt-90) REVERT: C 266 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8368 (tt) REVERT: C 357 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6401 (mtp) REVERT: D 215 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7668 (tm-30) REVERT: D 227 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.5827 (mmt-90) REVERT: D 385 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8076 (t0) REVERT: D 405 THR cc_start: 0.8849 (m) cc_final: 0.8639 (t) REVERT: E 266 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8474 (tt) REVERT: E 280 ASN cc_start: 0.7692 (m-40) cc_final: 0.7377 (m110) REVERT: E 370 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7305 (ttp-170) REVERT: E 385 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8245 (t0) REVERT: E 405 THR cc_start: 0.8917 (m) cc_final: 0.8662 (t) REVERT: F 227 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5557 (mmt-90) REVERT: F 266 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8276 (tt) REVERT: F 280 ASN cc_start: 0.7699 (m-40) cc_final: 0.7460 (m110) REVERT: F 357 MET cc_start: 0.7642 (tpp) cc_final: 0.7386 (tpp) REVERT: F 370 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8578 (ttt180) REVERT: F 405 THR cc_start: 0.8842 (m) cc_final: 0.8635 (t) REVERT: G 195 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: G 266 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8158 (tt) REVERT: G 362 LYS cc_start: 0.8556 (mttt) cc_final: 0.8292 (mttt) REVERT: G 424 MET cc_start: 0.8352 (mtm) cc_final: 0.8045 (ptp) REVERT: G 526 TYR cc_start: 0.9289 (m-80) cc_final: 0.8899 (m-80) REVERT: G 539 GLU cc_start: 0.7878 (tp30) cc_final: 0.7666 (tp30) REVERT: H 195 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7829 (p0) REVERT: H 227 ARG cc_start: 0.6785 (tpp-160) cc_final: 0.6412 (tpp-160) REVERT: H 266 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8517 (tt) REVERT: H 429 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6985 (mt-10) REVERT: I 195 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7764 (p0) REVERT: I 266 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8220 (tt) REVERT: I 280 ASN cc_start: 0.7540 (m-40) cc_final: 0.7180 (m110) REVERT: I 289 ASP cc_start: 0.7447 (m-30) cc_final: 0.6932 (m-30) REVERT: I 332 PHE cc_start: 0.8249 (t80) cc_final: 0.8018 (t80) REVERT: I 424 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7955 (ptp) REVERT: J 195 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7916 (p0) REVERT: J 303 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9088 (tp) REVERT: J 352 PHE cc_start: 0.7539 (m-80) cc_final: 0.7271 (m-80) REVERT: K 227 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6187 (mmt180) REVERT: K 303 LEU cc_start: 0.9187 (tp) cc_final: 0.8854 (tp) REVERT: K 362 LYS cc_start: 0.8549 (mttt) cc_final: 0.8239 (mttt) REVERT: K 370 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8204 (ttt180) REVERT: K 385 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8140 (t0) REVERT: K 410 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8910 (pt) REVERT: K 411 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8377 (p0) REVERT: K 424 MET cc_start: 0.8345 (mtm) cc_final: 0.7850 (ptp) REVERT: K 526 TYR cc_start: 0.9265 (m-80) cc_final: 0.9001 (m-80) REVERT: L 227 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5839 (mmt-90) REVERT: L 266 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8394 (tt) REVERT: L 423 GLU cc_start: 0.7936 (tt0) cc_final: 0.7714 (tt0) REVERT: L 474 TYR cc_start: 0.7381 (t80) cc_final: 0.7027 (t80) REVERT: M 195 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7787 (p0) REVERT: M 266 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8617 (tt) REVERT: M 352 PHE cc_start: 0.7502 (m-80) cc_final: 0.7274 (m-80) REVERT: M 359 LEU cc_start: 0.8995 (tt) cc_final: 0.8677 (tt) REVERT: M 411 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8101 (p0) REVERT: N 227 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.5571 (mmt-90) REVERT: N 266 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (tt) REVERT: N 377 GLU cc_start: 0.8431 (pt0) cc_final: 0.8033 (pt0) REVERT: N 539 GLU cc_start: 0.7976 (tp30) cc_final: 0.7694 (tp30) outliers start: 288 outliers final: 186 residues processed: 737 average time/residue: 0.4958 time to fit residues: 597.5292 Evaluate side-chains 715 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 495 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 474 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 227 ARG Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 317 ASN Chi-restraints excluded: chain O residue 335 SER Chi-restraints excluded: chain O residue 375 THR Chi-restraints excluded: chain O residue 408 THR Chi-restraints excluded: chain O residue 410 ILE Chi-restraints excluded: chain O residue 430 ASP Chi-restraints excluded: chain O residue 460 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 445 ASN Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 GLU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 357 MET Chi-restraints excluded: chain C residue 362 LYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 375 THR Chi-restraints excluded: chain D residue 385 ASN Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 408 THR Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 430 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 316 ASN Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 370 ARG Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 410 ILE Chi-restraints excluded: chain E residue 411 ASN Chi-restraints excluded: chain E residue 430 ASP Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 317 ASN Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 ILE Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 316 ASN Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 474 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 186 ILE Chi-restraints excluded: chain H residue 195 ASP Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 275 ILE Chi-restraints excluded: chain H residue 291 ILE Chi-restraints excluded: chain H residue 317 ASN Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 410 ILE Chi-restraints excluded: chain H residue 430 ASP Chi-restraints excluded: chain H residue 460 ILE Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 316 ASN Chi-restraints excluded: chain I residue 317 ASN Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 411 ASN Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 460 ILE Chi-restraints excluded: chain I residue 474 TYR Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 275 ILE Chi-restraints excluded: chain J residue 303 LEU Chi-restraints excluded: chain J residue 316 ASN Chi-restraints excluded: chain J residue 317 ASN Chi-restraints excluded: chain J residue 360 ASN Chi-restraints excluded: chain J residue 410 ILE Chi-restraints excluded: chain J residue 430 ASP Chi-restraints excluded: chain J residue 460 ILE Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 275 ILE Chi-restraints excluded: chain K residue 317 ASN Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 353 ILE Chi-restraints excluded: chain K residue 370 ARG Chi-restraints excluded: chain K residue 385 ASN Chi-restraints excluded: chain K residue 408 THR Chi-restraints excluded: chain K residue 410 ILE Chi-restraints excluded: chain K residue 411 ASN Chi-restraints excluded: chain K residue 429 GLU Chi-restraints excluded: chain K residue 430 ASP Chi-restraints excluded: chain K residue 445 ASN Chi-restraints excluded: chain K residue 460 ILE Chi-restraints excluded: chain K residue 471 ILE Chi-restraints excluded: chain K residue 474 TYR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 227 ARG Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain L residue 275 ILE Chi-restraints excluded: chain L residue 317 ASN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 408 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 411 ASN Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 430 ASP Chi-restraints excluded: chain L residue 460 ILE Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 195 ASP Chi-restraints excluded: chain M residue 227 ARG Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 317 ASN Chi-restraints excluded: chain M residue 353 ILE Chi-restraints excluded: chain M residue 375 THR Chi-restraints excluded: chain M residue 408 THR Chi-restraints excluded: chain M residue 410 ILE Chi-restraints excluded: chain M residue 411 ASN Chi-restraints excluded: chain M residue 430 ASP Chi-restraints excluded: chain M residue 460 ILE Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 227 ARG Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain N residue 275 ILE Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 316 ASN Chi-restraints excluded: chain N residue 335 SER Chi-restraints excluded: chain N residue 353 ILE Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 408 THR Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 430 ASP Chi-restraints excluded: chain N residue 460 ILE Chi-restraints excluded: chain N residue 474 TYR Chi-restraints excluded: chain N residue 489 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.8980 chunk 328 optimal weight: 0.7980 chunk 226 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 293 optimal weight: 0.7980 chunk 438 optimal weight: 0.9980 chunk 463 optimal weight: 0.4980 chunk 228 optimal weight: 2.9990 chunk 415 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN B 465 GLN B 516 GLN C 376 GLN ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN E 376 GLN F 376 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 GLN ** J 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 516 GLN K 376 GLN K 516 GLN ** L 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 376 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2213 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: