Starting phenix.real_space_refine on Sat Feb 17 11:54:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyw_27784/02_2024/8dyw_27784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyw_27784/02_2024/8dyw_27784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyw_27784/02_2024/8dyw_27784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyw_27784/02_2024/8dyw_27784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyw_27784/02_2024/8dyw_27784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dyw_27784/02_2024/8dyw_27784.pdb" } resolution = 3.72 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= -0.003 sd= 0.150 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 70 5.16 5 C 11574 2.51 5 N 3287 2.21 5 O 3563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 84": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 81": "OD1" <-> "OD2" Residue "N ASP 82": "OD1" <-> "OD2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 17": "OD1" <-> "OD2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 82": "OD1" <-> "OD2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O GLU 85": "OE1" <-> "OE2" Residue "O TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 1": "OD1" <-> "OD2" Residue "R TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 81": "OD1" <-> "OD2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "R PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 70": "OE1" <-> "OE2" Residue "T PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 85": "OE1" <-> "OE2" Residue "S ASP 86": "OD1" <-> "OD2" Residue "V ASP 17": "OD1" <-> "OD2" Residue "V PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 61": "OD1" <-> "OD2" Residue "U TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 85": "OE1" <-> "OE2" Residue "U ASP 86": "OD1" <-> "OD2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U ASP 100": "OD1" <-> "OD2" Residue "U TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 6": "OE1" <-> "OE2" Residue "W PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 53": "OD1" <-> "OD2" Residue "W TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18494 Number of models: 1 Model: "" Number of chains: 21 Chain: "I" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 564 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 20, 'TRANS': 59} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "F" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "M" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "P" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "O" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "R" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Q" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "T" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "S" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "V" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "U" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "X" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "W" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Time building chain proxies: 10.04, per 1000 atoms: 0.54 Number of scatterers: 18494 At special positions: 0 Unit cell: (120.75, 115, 188.6, 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 70 16.00 O 3563 8.00 N 3287 7.00 C 11574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 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: 7.18 Conformation dependent library (CDL) restraints added in 3.7 seconds 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4300 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 55 sheets defined 7.0% alpha, 38.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.709A pdb=" N THR H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.935A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.737A pdb=" N GLU A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.864A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.196A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.582A pdb=" N THR E 87 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.888A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.502A pdb=" N THR M 87 " --> pdb=" O ASP M 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.919A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.722A pdb=" N GLU O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 61 through 64 removed outlier: 3.601A pdb=" N GLU Q 64 " --> pdb=" O ASP Q 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 64' Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR Q 87 " --> pdb=" O ASP Q 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.748A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.600A pdb=" N THR S 87 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 83 removed outlier: 4.085A pdb=" N PHE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 64 removed outlier: 3.544A pdb=" N GLU U 64 " --> pdb=" O ASP U 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 61 through 64' Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'W' and resid 61 through 64 removed outlier: 3.525A pdb=" N GLU W 64 " --> pdb=" O ASP W 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 61 through 64' Processing helix chain 'W' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.630A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.587A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.587A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.622A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY H 10 " --> pdb=" O ILE H 110 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 18 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.558A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.807A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 97 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.807A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.513A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.958A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.949A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.539A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.898A pdb=" N THR D 97 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.867A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 18 through 21 Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.634A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.588A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.781A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.356A pdb=" N GLY E 10 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS E 35 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 18 through 21 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.706A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.515A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.515A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR N 97 " --> pdb=" O HIS N 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 3 through 4 removed outlier: 3.665A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY M 10 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 18 through 21 Processing sheet with id=AD2, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.956A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.547A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.797A pdb=" N THR P 97 " --> pdb=" O HIS P 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.711A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL O 5 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU O 78 " --> pdb=" O CYS O 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.338A pdb=" N GLY O 10 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS O 35 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.655A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.747A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.747A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR R 97 " --> pdb=" O HIS R 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 3 through 4 removed outlier: 3.893A pdb=" N GLN Q 3 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.808A pdb=" N MET Q 34 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 18 through 21 removed outlier: 3.780A pdb=" N THR Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP Q 72 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.617A pdb=" N VAL T 19 " --> pdb=" O ILE T 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.682A pdb=" N GLU T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.682A pdb=" N GLU T 105 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR T 97 " --> pdb=" O HIS T 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 3 through 4 removed outlier: 4.039A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY S 10 " --> pdb=" O ILE S 110 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N MET S 34 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 18 through 21 Processing sheet with id=AF1, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.514A pdb=" N CYS V 23 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE V 71 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.589A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.589A pdb=" N GLU V 105 " --> pdb=" O LEU V 11 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR V 97 " --> pdb=" O HIS V 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.509A pdb=" N GLY U 10 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS U 35 " --> pdb=" O ALA U 93 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET U 34 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 18 through 21 removed outlier: 3.564A pdb=" N THR U 77 " --> pdb=" O ASP U 72 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP U 72 " --> pdb=" O THR U 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 4 through 5 removed outlier: 3.644A pdb=" N GLU X 70 " --> pdb=" O SER X 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.858A pdb=" N LEU X 33 " --> pdb=" O TYR X 49 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR X 49 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 3 through 4 Processing sheet with id=AF9, first strand: chain 'W' and resid 10 through 12 removed outlier: 3.609A pdb=" N ALA W 88 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN W 39 " --> pdb=" O ILE W 89 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET W 34 " --> pdb=" O VAL W 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 18 through 21 648 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 1 1.12 - 1.30: 2984 1.30 - 1.47: 8276 1.47 - 1.65: 7562 1.65 - 1.83: 100 Bond restraints: 18923 Sorted by residual: bond pdb=" CB PRO A 41 " pdb=" CG PRO A 41 " ideal model delta sigma weight residual 1.492 0.945 0.547 5.00e-02 4.00e+02 1.20e+02 bond pdb=" CG PRO A 41 " pdb=" CD PRO A 41 " ideal model delta sigma weight residual 1.503 1.167 0.336 3.40e-02 8.65e+02 9.79e+01 bond pdb=" N PRO A 41 " pdb=" CA PRO A 41 " ideal model delta sigma weight residual 1.471 1.502 -0.032 1.32e-02 5.74e+03 5.74e+00 bond pdb=" CB PRO T 44 " pdb=" CG PRO T 44 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.27e+00 bond pdb=" CA PRO A 41 " pdb=" CB PRO A 41 " ideal model delta sigma weight residual 1.534 1.562 -0.029 1.40e-02 5.10e+03 4.17e+00 ... (remaining 18918 not shown) Histogram of bond angle deviations from ideal: 72.71 - 89.14: 2 89.14 - 105.56: 335 105.56 - 121.99: 20682 121.99 - 138.41: 4653 138.41 - 154.84: 1 Bond angle restraints: 25673 Sorted by residual: angle pdb=" N PRO A 41 " pdb=" CD PRO A 41 " pdb=" CG PRO A 41 " ideal model delta sigma weight residual 103.20 76.87 26.33 1.50e+00 4.44e-01 3.08e+02 angle pdb=" CA PRO A 41 " pdb=" CB PRO A 41 " pdb=" CG PRO A 41 " ideal model delta sigma weight residual 104.50 72.71 31.79 1.90e+00 2.77e-01 2.80e+02 angle pdb=" CB PRO A 41 " pdb=" CG PRO A 41 " pdb=" CD PRO A 41 " ideal model delta sigma weight residual 106.10 154.84 -48.74 3.20e+00 9.77e-02 2.32e+02 angle pdb=" CA PRO A 41 " pdb=" N PRO A 41 " pdb=" CD PRO A 41 " ideal model delta sigma weight residual 112.00 100.00 12.00 1.40e+00 5.10e-01 7.35e+01 angle pdb=" C GLN F 38 " pdb=" N LYS F 39 " pdb=" CA LYS F 39 " ideal model delta sigma weight residual 120.68 112.78 7.90 1.52e+00 4.33e-01 2.70e+01 ... (remaining 25668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9878 17.96 - 35.93: 973 35.93 - 53.89: 215 53.89 - 71.85: 39 71.85 - 89.82: 16 Dihedral angle restraints: 11121 sinusoidal: 4352 harmonic: 6769 Sorted by residual: dihedral pdb=" CB CYS W 22 " pdb=" SG CYS W 22 " pdb=" SG CYS W 92 " pdb=" CB CYS W 92 " ideal model delta sinusoidal sigma weight residual -86.00 -1.67 -84.33 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" N PRO A 41 " pdb=" CG PRO A 41 " pdb=" CD PRO A 41 " pdb=" CB PRO A 41 " ideal model delta sinusoidal sigma weight residual 30.00 114.23 -84.23 1 1.50e+01 4.44e-03 3.84e+01 dihedral pdb=" CB CYS V 23 " pdb=" SG CYS V 23 " pdb=" SG CYS V 88 " pdb=" CB CYS V 88 " ideal model delta sinusoidal sigma weight residual 93.00 49.94 43.06 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 11118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2259 0.052 - 0.105: 391 0.105 - 0.157: 98 0.157 - 0.209: 2 0.209 - 0.262: 2 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CB ILE U 89 " pdb=" CA ILE U 89 " pdb=" CG1 ILE U 89 " pdb=" CG2 ILE U 89 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CG LEU P 11 " pdb=" CB LEU P 11 " pdb=" CD1 LEU P 11 " pdb=" CD2 LEU P 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE C 89 " pdb=" CA ILE C 89 " pdb=" CG1 ILE C 89 " pdb=" CG2 ILE C 89 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2749 not shown) Planarity restraints: 3329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " 0.066 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO D 80 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 79 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO N 80 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO N 80 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO N 80 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA T 43 " -0.059 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO T 44 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO T 44 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO T 44 " -0.047 5.00e-02 4.00e+02 ... (remaining 3326 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 456 2.68 - 3.23: 17566 3.23 - 3.79: 29240 3.79 - 4.34: 40137 4.34 - 4.90: 66657 Nonbonded interactions: 154056 Sorted by model distance: nonbonded pdb=" O ASP X 82 " pdb=" OH TYR X 86 " model vdw 2.122 2.440 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.127 2.440 nonbonded pdb=" OE2 GLU U 6 " pdb=" N GLY U 106 " model vdw 2.139 2.520 nonbonded pdb=" OE1 GLN D 6 " pdb=" OG1 THR D 102 " model vdw 2.166 2.440 nonbonded pdb=" N GLU U 6 " pdb=" OE1 GLU U 6 " model vdw 2.167 2.520 ... (remaining 154051 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 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 0.510 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: 3.420 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 50.750 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.180 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 0.547 18923 Z= 0.302 Angle : 0.847 48.738 25673 Z= 0.445 Chirality : 0.044 0.262 2752 Planarity : 0.005 0.099 3329 Dihedral : 15.005 89.817 6761 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Rotamer: Outliers : 0.30 % Allowed : 17.18 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.02 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.23 (0.16), residues: 1150 loop : -0.08 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP W 36 HIS 0.004 0.001 HIS X 90 PHE 0.022 0.002 PHE X 71 TYR 0.030 0.001 TYR T 91 ARG 0.016 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.124 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 70 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6645 (mm-30) REVERT: R 78 LEU cc_start: 0.8990 (tt) cc_final: 0.8724 (mp) REVERT: V 70 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8076 (mp0) outliers start: 6 outliers final: 5 residues processed: 256 average time/residue: 0.3709 time to fit residues: 134.8655 Evaluate side-chains 234 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 1 GLN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain X residue 50 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 40.0000 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 50.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN F 3 GLN ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN T 38 GLN T 89 GLN ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18923 Z= 0.250 Angle : 0.600 8.488 25673 Z= 0.316 Chirality : 0.044 0.236 2752 Planarity : 0.004 0.066 3329 Dihedral : 4.951 56.718 2642 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Rotamer: Outliers : 2.25 % Allowed : 15.63 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.17 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.35 (0.16), residues: 1160 loop : -0.01 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 35 HIS 0.003 0.001 HIS O 35 PHE 0.017 0.002 PHE H 29 TYR 0.019 0.001 TYR X 87 ARG 0.007 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 2.191 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: symmetry clash revert: symmetry clash REVERT: M 79 TYR cc_start: 0.8679 (m-80) cc_final: 0.8362 (m-80) REVERT: R 18 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7833 (ttp80) REVERT: R 78 LEU cc_start: 0.8904 (tt) cc_final: 0.8700 (mp) REVERT: R 89 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8577 (tm-30) REVERT: R 100 GLN cc_start: 0.8403 (mp10) cc_final: 0.8146 (pm20) REVERT: Q 100 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: U 79 TYR cc_start: 0.7192 (m-80) cc_final: 0.6901 (m-80) REVERT: U 108 LEU cc_start: 0.8476 (tt) cc_final: 0.8104 (mp) REVERT: X 50 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: X 98 PHE cc_start: 0.4776 (OUTLIER) cc_final: 0.4396 (m-10) outliers start: 45 outliers final: 19 residues processed: 275 average time/residue: 0.3681 time to fit residues: 144.8700 Evaluate side-chains 245 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 82 MET Chi-restraints excluded: chain X residue 50 GLN Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 207 optimal weight: 50.0000 chunk 224 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN A 31 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN T 89 GLN ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 18923 Z= 0.439 Angle : 0.641 8.300 25673 Z= 0.342 Chirality : 0.045 0.239 2752 Planarity : 0.005 0.060 3329 Dihedral : 4.878 40.083 2632 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.20 % Favored : 94.37 % Rotamer: Outliers : 3.65 % Allowed : 15.88 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.04 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.23 (0.16), residues: 1040 loop : -0.14 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.010 0.001 HIS R 90 PHE 0.028 0.002 PHE H 29 TYR 0.020 0.002 TYR R 49 ARG 0.006 0.001 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 222 time to evaluate : 2.016 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: symmetry clash REVERT: L 81 ASP cc_start: 0.8399 (t0) cc_final: 0.7936 (m-30) REVERT: H 91 TYR cc_start: 0.8463 (m-80) cc_final: 0.8242 (m-80) REVERT: D 4 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7406 (mmm) REVERT: C 71 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7445 (ttm-80) REVERT: C 110 ILE cc_start: 0.9084 (mm) cc_final: 0.8852 (tp) REVERT: M 71 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7483 (ttm-80) REVERT: O 100 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8175 (m-30) REVERT: R 18 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7784 (ttp80) REVERT: R 89 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8755 (tm-30) REVERT: Q 100 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: S 95 ASP cc_start: 0.7167 (t0) cc_final: 0.6889 (t0) REVERT: U 108 LEU cc_start: 0.8473 (tt) cc_final: 0.8172 (mp) REVERT: X 98 PHE cc_start: 0.5003 (OUTLIER) cc_final: 0.4444 (m-80) outliers start: 73 outliers final: 37 residues processed: 275 average time/residue: 0.3769 time to fit residues: 147.0605 Evaluate side-chains 253 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 110 ILE Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 100 ASP Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 80 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 63 ASN L 3 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN R 89 GLN T 89 GLN S 13 GLN ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18923 Z= 0.244 Angle : 0.571 8.622 25673 Z= 0.301 Chirality : 0.043 0.194 2752 Planarity : 0.004 0.053 3329 Dihedral : 4.478 19.497 2629 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.87 % Favored : 95.70 % Rotamer: Outliers : 3.70 % Allowed : 15.98 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.01 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.25 (0.16), residues: 1040 loop : -0.09 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 35 HIS 0.006 0.001 HIS R 90 PHE 0.023 0.002 PHE C 100D TYR 0.014 0.001 TYR X 87 ARG 0.007 0.000 ARG Q 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 236 time to evaluate : 2.113 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 ASP cc_start: 0.8477 (t0) cc_final: 0.7937 (m-30) REVERT: H 91 TYR cc_start: 0.8400 (m-80) cc_final: 0.8119 (m-80) REVERT: D 1 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: D 4 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7856 (tpp) REVERT: C 71 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.7377 (ttm-80) REVERT: E 3 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: E 28 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8208 (p) REVERT: R 18 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7862 (ttp80) REVERT: R 89 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8855 (tm-30) REVERT: Q 79 TYR cc_start: 0.7954 (m-80) cc_final: 0.7408 (m-80) REVERT: Q 100 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: T 33 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7637 (mp) REVERT: T 89 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: S 95 ASP cc_start: 0.7190 (t0) cc_final: 0.6949 (t0) REVERT: V 4 MET cc_start: 0.7922 (tpp) cc_final: 0.7716 (tpp) REVERT: V 50 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8364 (tp-100) REVERT: U 108 LEU cc_start: 0.8422 (tt) cc_final: 0.8190 (mp) REVERT: X 86 TYR cc_start: 0.5869 (m-80) cc_final: 0.5602 (m-80) REVERT: X 98 PHE cc_start: 0.5188 (OUTLIER) cc_final: 0.4955 (m-80) outliers start: 74 outliers final: 41 residues processed: 287 average time/residue: 0.3620 time to fit residues: 148.8388 Evaluate side-chains 264 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 213 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 89 GLN Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 3 optimal weight: 0.0870 chunk 164 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 55 optimal weight: 0.0870 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN R 89 GLN T 89 GLN ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18923 Z= 0.192 Angle : 0.556 8.698 25673 Z= 0.289 Chirality : 0.043 0.234 2752 Planarity : 0.004 0.050 3329 Dihedral : 4.280 18.818 2629 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.69 % Favored : 95.88 % Rotamer: Outliers : 3.60 % Allowed : 17.13 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.11 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.44 (0.16), residues: 1020 loop : -0.14 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W 103 HIS 0.005 0.001 HIS R 90 PHE 0.019 0.001 PHE S 67 TYR 0.011 0.001 TYR S 79 ARG 0.008 0.000 ARG Q 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 240 time to evaluate : 2.212 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: symmetry clash revert: symmetry clash REVERT: I 79 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.5881 (p0) REVERT: L 81 ASP cc_start: 0.8509 (t0) cc_final: 0.8226 (t0) REVERT: H 91 TYR cc_start: 0.8248 (m-80) cc_final: 0.7930 (m-80) REVERT: A 102 TYR cc_start: 0.7772 (m-10) cc_final: 0.7558 (m-10) REVERT: D 1 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8475 (m-30) REVERT: C 71 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7366 (ttm-80) REVERT: F 33 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8104 (mt) REVERT: E 3 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: M 79 TYR cc_start: 0.8668 (m-80) cc_final: 0.8211 (m-80) REVERT: R 18 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7931 (ttp80) REVERT: Q 37 VAL cc_start: 0.9135 (t) cc_final: 0.8935 (m) REVERT: Q 79 TYR cc_start: 0.7983 (m-80) cc_final: 0.7455 (m-80) REVERT: Q 100 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8815 (m-80) REVERT: T 33 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7569 (mp) REVERT: S 95 ASP cc_start: 0.7150 (t0) cc_final: 0.6906 (t0) REVERT: V 3 GLN cc_start: 0.8523 (pm20) cc_final: 0.8297 (pp30) REVERT: V 50 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8152 (tp-100) REVERT: V 103 ARG cc_start: 0.8027 (tpt-90) cc_final: 0.7699 (tpt-90) REVERT: X 86 TYR cc_start: 0.5854 (m-80) cc_final: 0.5471 (m-80) outliers start: 72 outliers final: 41 residues processed: 287 average time/residue: 0.3707 time to fit residues: 151.7942 Evaluate side-chains 269 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain D residue 1 ASP Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 220 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 37 GLN B 89 GLN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN R 27 GLN R 89 GLN T 89 GLN V 38 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 18923 Z= 0.545 Angle : 0.690 8.747 25673 Z= 0.367 Chirality : 0.047 0.329 2752 Planarity : 0.005 0.054 3329 Dihedral : 4.972 20.910 2629 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.93 % Favored : 93.64 % Rotamer: Outliers : 4.20 % Allowed : 16.98 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.27 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.10 (0.17), residues: 1030 loop : -0.33 (0.18), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.007 0.002 HIS R 90 PHE 0.027 0.003 PHE O 29 TYR 0.026 0.002 TYR T 49 ARG 0.011 0.001 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 213 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 79 ASN cc_start: 0.6479 (OUTLIER) cc_final: 0.5914 (p0) REVERT: L 81 ASP cc_start: 0.8569 (t0) cc_final: 0.8111 (m-30) REVERT: H 91 TYR cc_start: 0.8543 (m-80) cc_final: 0.8124 (m-80) REVERT: B 89 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6942 (tm-30) REVERT: D 4 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7463 (mmm) REVERT: C 71 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.7499 (ttm-80) REVERT: C 89 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8949 (tp) REVERT: C 100 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9201 (m-80) REVERT: E 28 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8244 (p) REVERT: R 18 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7883 (ttp80) REVERT: Q 100 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8742 (m-80) REVERT: T 89 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: T 105 GLU cc_start: 0.2434 (tp30) cc_final: 0.2094 (tp30) REVERT: S 82 MET cc_start: 0.8252 (mmm) cc_final: 0.7959 (tpp) REVERT: S 95 ASP cc_start: 0.7415 (t0) cc_final: 0.7105 (t0) REVERT: V 3 GLN cc_start: 0.8521 (pm20) cc_final: 0.8311 (pp30) REVERT: V 50 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8210 (tp40) REVERT: X 86 TYR cc_start: 0.5762 (m-80) cc_final: 0.5453 (m-80) REVERT: W 30 ARG cc_start: 0.7194 (ptm-80) cc_final: 0.6977 (ptm-80) outliers start: 84 outliers final: 56 residues processed: 274 average time/residue: 0.3634 time to fit residues: 142.4177 Evaluate side-chains 264 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 199 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain P residue 17 ASP Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain U residue 110 ILE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 50.0000 chunk 24 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 50.0000 chunk 123 optimal weight: 4.9990 chunk 219 optimal weight: 50.0000 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN X 50 GLN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18923 Z= 0.202 Angle : 0.582 9.271 25673 Z= 0.303 Chirality : 0.044 0.266 2752 Planarity : 0.004 0.049 3329 Dihedral : 4.455 19.191 2629 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.52 % Favored : 96.05 % Rotamer: Outliers : 3.35 % Allowed : 17.98 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.06 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 1000 loop : -0.17 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.005 0.001 HIS C 35 PHE 0.018 0.001 PHE V 71 TYR 0.019 0.001 TYR S 91 ARG 0.014 0.000 ARG T 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 225 time to evaluate : 2.038 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: I 79 ASN cc_start: 0.6391 (OUTLIER) cc_final: 0.5953 (p0) REVERT: L 81 ASP cc_start: 0.8597 (t0) cc_final: 0.8354 (t0) REVERT: H 91 TYR cc_start: 0.8341 (m-80) cc_final: 0.7914 (m-80) REVERT: A 102 TYR cc_start: 0.7879 (m-80) cc_final: 0.7570 (m-10) REVERT: D 4 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7946 (tpp) REVERT: D 27 GLN cc_start: 0.9247 (pm20) cc_final: 0.8713 (pm20) REVERT: C 71 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7367 (ttm-80) REVERT: C 100 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: E 28 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8178 (p) REVERT: M 79 TYR cc_start: 0.8684 (m-80) cc_final: 0.8227 (m-80) REVERT: O 28 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7914 (t) REVERT: Q 79 TYR cc_start: 0.8027 (m-80) cc_final: 0.7569 (m-80) REVERT: Q 100 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: T 105 GLU cc_start: 0.2206 (tp30) cc_final: 0.1915 (tp30) REVERT: S 71 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7720 (ttm170) REVERT: S 95 ASP cc_start: 0.7517 (t0) cc_final: 0.7148 (t0) REVERT: V 50 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8131 (tp40) REVERT: X 86 TYR cc_start: 0.5672 (m-80) cc_final: 0.5261 (m-80) REVERT: W 96 TRP cc_start: 0.6401 (t-100) cc_final: 0.5897 (t-100) outliers start: 67 outliers final: 41 residues processed: 273 average time/residue: 0.3639 time to fit residues: 142.3803 Evaluate side-chains 263 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18923 Z= 0.215 Angle : 0.581 9.923 25673 Z= 0.300 Chirality : 0.044 0.366 2752 Planarity : 0.004 0.050 3329 Dihedral : 4.309 21.704 2629 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.08 % Favored : 95.49 % Rotamer: Outliers : 2.80 % Allowed : 18.88 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.02 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.39 (0.17), residues: 950 loop : -0.24 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 52 HIS 0.006 0.001 HIS C 35 PHE 0.023 0.002 PHE X 71 TYR 0.017 0.001 TYR S 91 ARG 0.009 0.000 ARG Q 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 222 time to evaluate : 2.984 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: I 79 ASN cc_start: 0.6267 (OUTLIER) cc_final: 0.5802 (p0) REVERT: L 81 ASP cc_start: 0.8619 (t0) cc_final: 0.8320 (t0) REVERT: H 91 TYR cc_start: 0.8284 (m-80) cc_final: 0.7851 (m-80) REVERT: A 102 TYR cc_start: 0.7859 (m-80) cc_final: 0.7551 (m-10) REVERT: D 4 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7914 (tpp) REVERT: C 71 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7385 (ttm-80) REVERT: C 89 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8907 (tp) REVERT: C 100 PHE cc_start: 0.9245 (OUTLIER) cc_final: 0.8982 (m-80) REVERT: F 105 GLU cc_start: 0.6708 (tp30) cc_final: 0.6454 (tp30) REVERT: E 28 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8168 (p) REVERT: M 34 MET cc_start: 0.8545 (mmm) cc_final: 0.8316 (mmt) REVERT: M 79 TYR cc_start: 0.8637 (m-80) cc_final: 0.8190 (m-80) REVERT: O 28 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7903 (t) REVERT: Q 37 VAL cc_start: 0.9112 (t) cc_final: 0.8884 (m) REVERT: Q 79 TYR cc_start: 0.8096 (m-80) cc_final: 0.7723 (m-80) REVERT: Q 100 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: S 71 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: S 95 ASP cc_start: 0.7437 (t0) cc_final: 0.7183 (t0) REVERT: V 3 GLN cc_start: 0.8491 (pm20) cc_final: 0.8242 (pp30) REVERT: V 50 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8144 (tp40) REVERT: V 103 ARG cc_start: 0.8131 (tpt-90) cc_final: 0.7878 (mmm160) REVERT: X 86 TYR cc_start: 0.5960 (m-80) cc_final: 0.5563 (m-80) REVERT: W 96 TRP cc_start: 0.6348 (t-100) cc_final: 0.5858 (t-100) outliers start: 56 outliers final: 40 residues processed: 263 average time/residue: 0.3812 time to fit residues: 142.3174 Evaluate side-chains 260 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 82 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 7.9990 chunk 210 optimal weight: 50.0000 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 185 optimal weight: 50.0000 chunk 193 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18923 Z= 0.303 Angle : 0.611 10.247 25673 Z= 0.316 Chirality : 0.044 0.352 2752 Planarity : 0.004 0.051 3329 Dihedral : 4.419 19.988 2629 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.42 % Favored : 95.15 % Rotamer: Outliers : 3.15 % Allowed : 18.68 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.02 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 940 loop : -0.19 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 35 HIS 0.006 0.001 HIS C 35 PHE 0.015 0.002 PHE W 58 TYR 0.017 0.001 TYR S 91 ARG 0.008 0.000 ARG R 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 214 time to evaluate : 2.401 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: I 79 ASN cc_start: 0.6259 (OUTLIER) cc_final: 0.5706 (p0) REVERT: L 81 ASP cc_start: 0.8584 (t0) cc_final: 0.8259 (t0) REVERT: H 91 TYR cc_start: 0.8334 (m-80) cc_final: 0.7899 (m-80) REVERT: D 4 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7934 (tpp) REVERT: D 18 ARG cc_start: 0.8006 (tpp80) cc_final: 0.7588 (mmm-85) REVERT: C 71 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7439 (ttm-80) REVERT: C 89 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8893 (tp) REVERT: C 100 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9099 (m-80) REVERT: F 105 GLU cc_start: 0.6723 (tp30) cc_final: 0.6456 (tp30) REVERT: E 28 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (p) REVERT: E 82 MET cc_start: 0.8492 (mmt) cc_final: 0.8080 (mmt) REVERT: M 34 MET cc_start: 0.8588 (mmm) cc_final: 0.8361 (mmt) REVERT: M 79 TYR cc_start: 0.8682 (m-80) cc_final: 0.8239 (m-80) REVERT: O 28 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7918 (t) REVERT: Q 79 TYR cc_start: 0.8125 (m-80) cc_final: 0.7722 (m-80) REVERT: Q 100 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: S 71 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7845 (ttm170) REVERT: S 75 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8381 (ptpp) REVERT: S 95 ASP cc_start: 0.7553 (t0) cc_final: 0.7260 (t0) REVERT: V 50 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8214 (tp40) REVERT: U 82 MET cc_start: 0.7258 (mmm) cc_final: 0.6870 (mmm) REVERT: X 4 MET cc_start: 0.3758 (mtm) cc_final: 0.3294 (mtm) REVERT: X 86 TYR cc_start: 0.5961 (m-80) cc_final: 0.5570 (m-80) REVERT: W 30 ARG cc_start: 0.7130 (ptm-80) cc_final: 0.6885 (ptm-80) REVERT: W 96 TRP cc_start: 0.6365 (t-100) cc_final: 0.5272 (t-100) outliers start: 63 outliers final: 46 residues processed: 259 average time/residue: 0.3680 time to fit residues: 137.8966 Evaluate side-chains 264 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 209 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 45 ASN Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 0.0570 chunk 102 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18923 Z= 0.245 Angle : 0.606 12.190 25673 Z= 0.310 Chirality : 0.044 0.317 2752 Planarity : 0.004 0.050 3329 Dihedral : 4.341 23.100 2629 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.30 % Favored : 95.27 % Rotamer: Outliers : 2.90 % Allowed : 18.98 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.03 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.40 (0.17), residues: 940 loop : -0.18 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 35 HIS 0.006 0.001 HIS C 35 PHE 0.022 0.002 PHE X 71 TYR 0.015 0.001 TYR S 91 ARG 0.009 0.000 ARG R 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4656 Ramachandran restraints generated. 2328 Oldfield, 0 Emsley, 2328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 219 time to evaluate : 2.141 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: I 79 ASN cc_start: 0.6131 (OUTLIER) cc_final: 0.5542 (p0) REVERT: L 81 ASP cc_start: 0.8599 (t0) cc_final: 0.8304 (t0) REVERT: H 91 TYR cc_start: 0.8296 (m-80) cc_final: 0.7860 (m-80) REVERT: D 4 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: D 18 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7652 (mmm-85) REVERT: D 27 GLN cc_start: 0.9262 (pm20) cc_final: 0.8745 (pm20) REVERT: C 71 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.7414 (ttm-80) REVERT: C 89 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8881 (tp) REVERT: C 100 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.9065 (m-80) REVERT: F 105 GLU cc_start: 0.6698 (tp30) cc_final: 0.6431 (tp30) REVERT: E 28 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8187 (p) REVERT: E 82 MET cc_start: 0.8479 (mmt) cc_final: 0.8045 (mmt) REVERT: M 34 MET cc_start: 0.8553 (mmm) cc_final: 0.8331 (mmt) REVERT: M 79 TYR cc_start: 0.8653 (m-80) cc_final: 0.8196 (m-80) REVERT: O 28 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7903 (t) REVERT: Q 79 TYR cc_start: 0.8093 (m-80) cc_final: 0.7715 (m-80) REVERT: Q 100 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: S 71 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7827 (ttm170) REVERT: S 75 LYS cc_start: 0.8656 (ptpp) cc_final: 0.8392 (ptpp) REVERT: S 95 ASP cc_start: 0.7588 (t0) cc_final: 0.7318 (t0) REVERT: V 50 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8341 (tp40) REVERT: U 82 MET cc_start: 0.7165 (mmm) cc_final: 0.6849 (mmm) REVERT: X 4 MET cc_start: 0.3847 (mtm) cc_final: 0.3381 (mtm) REVERT: X 86 TYR cc_start: 0.6117 (m-80) cc_final: 0.5499 (m-80) REVERT: X 98 PHE cc_start: 0.5160 (OUTLIER) cc_final: 0.4609 (m-80) REVERT: W 30 ARG cc_start: 0.7126 (ptm-80) cc_final: 0.6874 (ptm-80) outliers start: 58 outliers final: 45 residues processed: 261 average time/residue: 0.3644 time to fit residues: 136.3168 Evaluate side-chains 267 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 212 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 79 ASN Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain B residue 90 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 PHE Chi-restraints excluded: chain R residue 17 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 90 HIS Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 100 PHE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 ARG Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 100 PHE Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain U residue 11 VAL Chi-restraints excluded: chain U residue 27 LEU Chi-restraints excluded: chain U residue 78 LEU Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain U residue 100 PHE Chi-restraints excluded: chain X residue 6 GLN Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 98 PHE Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 35 HIS Chi-restraints excluded: chain W residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 55 optimal weight: 0.0370 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.089353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065698 restraints weight = 53155.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067028 restraints weight = 48321.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.067036 restraints weight = 46339.683| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18923 Z= 0.318 Angle : 0.636 14.378 25673 Z= 0.326 Chirality : 0.044 0.313 2752 Planarity : 0.004 0.051 3329 Dihedral : 4.461 24.569 2629 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.81 % Favored : 94.76 % Rotamer: Outliers : 3.00 % Allowed : 18.88 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.02 (0.18), residues: 2328 helix: None (None), residues: 0 sheet: 0.37 (0.17), residues: 940 loop : -0.22 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP W 96 HIS 0.006 0.001 HIS C 35 PHE 0.015 0.002 PHE O 29 TYR 0.017 0.001 TYR R 49 ARG 0.009 0.001 ARG R 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3444.27 seconds wall clock time: 64 minutes 15.61 seconds (3855.61 seconds total)