Starting phenix.real_space_refine on Sun Feb 18 03:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/02_2024/7l85_23222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/02_2024/7l85_23222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/02_2024/7l85_23222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/02_2024/7l85_23222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/02_2024/7l85_23222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/02_2024/7l85_23222.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 13104 2.51 5 N 3552 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "I TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "K TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "O TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "Q TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "S TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "V TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "X TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20556 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "D" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "E" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "G" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "H" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "I" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "M" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "N" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "O" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "P" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "R" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "S" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "T" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "V" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "W" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "X" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "Y" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Time building chain proxies: 10.43, per 1000 atoms: 0.51 Number of scatterers: 20556 At special positions: 0 Unit cell: (126.5, 127.65, 125.35, 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 36 16.00 O 3864 8.00 N 3552 7.00 C 13104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.96 Conformation dependent library (CDL) restraints added in 3.8 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 36.5% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'B' and resid 16 through 35 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 58 through 64 removed outlier: 4.121A pdb=" N ALA B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 64' Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.541A pdb=" N VAL B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'C' and resid 16 through 35 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 64' Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL C 113 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'E' and resid 16 through 35 Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 63 " --> pdb=" O PRO E 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 64' Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL E 113 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 26 Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 92 through 102 Processing helix chain 'G' and resid 16 through 35 Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.121A pdb=" N ALA G 62 " --> pdb=" O PHE G 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 63 " --> pdb=" O PRO G 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 64' Processing helix chain 'G' and resid 100 through 104 Processing helix chain 'G' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL G 113 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 64 through 76 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'I' and resid 16 through 35 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 58 through 64 removed outlier: 4.121A pdb=" N ALA I 62 " --> pdb=" O PHE I 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 63 " --> pdb=" O PRO I 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 64' Processing helix chain 'I' and resid 100 through 104 Processing helix chain 'I' and resid 110 through 116 removed outlier: 3.539A pdb=" N VAL I 113 " --> pdb=" O ASN I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 26 Processing helix chain 'J' and resid 64 through 76 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'K' and resid 16 through 35 Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA K 62 " --> pdb=" O PHE K 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 63 " --> pdb=" O PRO K 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 64' Processing helix chain 'K' and resid 100 through 104 Processing helix chain 'K' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL K 113 " --> pdb=" O ASN K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 26 Processing helix chain 'L' and resid 64 through 76 Processing helix chain 'L' and resid 92 through 102 Processing helix chain 'M' and resid 16 through 35 Processing helix chain 'M' and resid 39 through 41 No H-bonds generated for 'chain 'M' and resid 39 through 41' Processing helix chain 'M' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA M 62 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 58 through 64' Processing helix chain 'M' and resid 100 through 104 Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL M 113 " --> pdb=" O ASN M 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 26 Processing helix chain 'N' and resid 64 through 76 Processing helix chain 'N' and resid 92 through 102 Processing helix chain 'O' and resid 16 through 35 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA O 62 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 64' Processing helix chain 'O' and resid 100 through 104 Processing helix chain 'O' and resid 110 through 116 removed outlier: 3.539A pdb=" N VAL O 113 " --> pdb=" O ASN O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 26 Processing helix chain 'P' and resid 64 through 76 Processing helix chain 'P' and resid 92 through 102 Processing helix chain 'Q' and resid 16 through 35 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA Q 62 " --> pdb=" O PHE Q 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Q 63 " --> pdb=" O PRO Q 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 58 through 64' Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL Q 113 " --> pdb=" O ASN Q 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 26 Processing helix chain 'R' and resid 64 through 76 Processing helix chain 'R' and resid 92 through 102 Processing helix chain 'S' and resid 16 through 35 Processing helix chain 'S' and resid 39 through 41 No H-bonds generated for 'chain 'S' and resid 39 through 41' Processing helix chain 'S' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA S 62 " --> pdb=" O PHE S 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA S 63 " --> pdb=" O PRO S 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG S 64 " --> pdb=" O ALA S 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 58 through 64' Processing helix chain 'S' and resid 100 through 104 Processing helix chain 'S' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL S 113 " --> pdb=" O ASN S 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 26 Processing helix chain 'T' and resid 64 through 76 Processing helix chain 'T' and resid 92 through 102 Processing helix chain 'V' and resid 16 through 35 Processing helix chain 'V' and resid 39 through 41 No H-bonds generated for 'chain 'V' and resid 39 through 41' Processing helix chain 'V' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA V 62 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA V 63 " --> pdb=" O PRO V 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG V 64 " --> pdb=" O ALA V 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 58 through 64' Processing helix chain 'V' and resid 100 through 104 Processing helix chain 'V' and resid 110 through 116 removed outlier: 3.539A pdb=" N VAL V 113 " --> pdb=" O ASN V 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 26 Processing helix chain 'W' and resid 64 through 76 Processing helix chain 'W' and resid 92 through 102 Processing helix chain 'X' and resid 16 through 35 Processing helix chain 'X' and resid 39 through 41 No H-bonds generated for 'chain 'X' and resid 39 through 41' Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA X 62 " --> pdb=" O PHE X 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA X 63 " --> pdb=" O PRO X 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 58 through 64' Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'X' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL X 113 " --> pdb=" O ASN X 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 26 Processing helix chain 'Y' and resid 64 through 76 Processing helix chain 'Y' and resid 92 through 102 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA B 45 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL B 107 " --> pdb=" O GLY B 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 7 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU B 109 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 9 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'W' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS A 31 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Y 90 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS Y 31 " --> pdb=" O LYS Y 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU W 90 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.530A pdb=" N GLU A 90 " --> pdb=" O ALA W 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS W 31 " --> pdb=" O LYS W 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA C 45 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL C 107 " --> pdb=" O GLY C 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG C 7 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU C 109 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 9 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 47 through 51 removed outlier: 3.527A pdb=" N CYS D 31 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU T 90 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS T 31 " --> pdb=" O LYS T 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU R 90 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.549A pdb=" N GLU D 90 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS R 31 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA E 45 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL E 107 " --> pdb=" O GLY E 5 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG E 7 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU E 109 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA E 9 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 90 through 91 removed outlier: 3.527A pdb=" N GLU J 90 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS F 31 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS J 31 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU N 90 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.562A pdb=" N GLU F 90 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS N 31 " --> pdb=" O LYS N 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA G 45 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL G 107 " --> pdb=" O GLY G 5 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG G 7 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU G 109 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA G 9 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS H 31 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 90 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 51 removed outlier: 3.529A pdb=" N CYS P 31 " --> pdb=" O LYS P 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU L 90 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.530A pdb=" N GLU H 90 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS L 31 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA I 45 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL I 107 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG I 7 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU I 109 " --> pdb=" O ARG I 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA I 9 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA K 45 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL K 107 " --> pdb=" O GLY K 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG K 7 " --> pdb=" O VAL K 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU K 109 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA K 9 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA M 45 " --> pdb=" O LEU M 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL M 107 " --> pdb=" O GLY M 5 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG M 7 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU M 109 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA M 9 " --> pdb=" O LEU M 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA O 45 " --> pdb=" O LEU O 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL O 107 " --> pdb=" O GLY O 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG O 7 " --> pdb=" O VAL O 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU O 109 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA O 9 " --> pdb=" O LEU O 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA Q 45 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL Q 107 " --> pdb=" O GLY Q 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG Q 7 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU Q 109 " --> pdb=" O ARG Q 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA S 45 " --> pdb=" O LEU S 94 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL S 107 " --> pdb=" O GLY S 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG S 7 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU S 109 " --> pdb=" O ARG S 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA S 9 " --> pdb=" O LEU S 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA V 45 " --> pdb=" O LEU V 94 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL V 107 " --> pdb=" O GLY V 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG V 7 " --> pdb=" O VAL V 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU V 109 " --> pdb=" O ARG V 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA V 9 " --> pdb=" O LEU V 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 73 through 77 removed outlier: 3.627A pdb=" N ALA X 45 " --> pdb=" O LEU X 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL X 107 " --> pdb=" O GLY X 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG X 7 " --> pdb=" O VAL X 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU X 109 " --> pdb=" O ARG X 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA X 9 " --> pdb=" O LEU X 109 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 3024 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: 6.87 Time building geometry restraints manager: 8.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4436 1.31 - 1.43: 4397 1.43 - 1.56: 11996 1.56 - 1.68: 15 1.68 - 1.80: 60 Bond restraints: 20904 Sorted by residual: bond pdb=" CB TYR P 95 " pdb=" CG TYR P 95 " ideal model delta sigma weight residual 1.512 1.418 0.094 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR N 95 " pdb=" CG TYR N 95 " ideal model delta sigma weight residual 1.512 1.418 0.094 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR T 95 " pdb=" CG TYR T 95 " ideal model delta sigma weight residual 1.512 1.419 0.093 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR D 95 " pdb=" CG TYR D 95 " ideal model delta sigma weight residual 1.512 1.419 0.093 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR H 95 " pdb=" CG TYR H 95 " ideal model delta sigma weight residual 1.512 1.419 0.093 2.20e-02 2.07e+03 1.80e+01 ... (remaining 20899 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.22: 1207 107.22 - 113.92: 11561 113.92 - 120.62: 9290 120.62 - 127.32: 6323 127.32 - 134.03: 155 Bond angle restraints: 28536 Sorted by residual: angle pdb=" C THR Q 99 " pdb=" N PRO Q 100 " pdb=" CA PRO Q 100 " ideal model delta sigma weight residual 119.78 126.91 -7.13 1.03e+00 9.43e-01 4.80e+01 angle pdb=" C THR E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta sigma weight residual 119.78 126.89 -7.11 1.03e+00 9.43e-01 4.76e+01 angle pdb=" C THR K 99 " pdb=" N PRO K 100 " pdb=" CA PRO K 100 " ideal model delta sigma weight residual 119.78 126.88 -7.10 1.03e+00 9.43e-01 4.76e+01 angle pdb=" C THR O 99 " pdb=" N PRO O 100 " pdb=" CA PRO O 100 " ideal model delta sigma weight residual 119.78 126.88 -7.10 1.03e+00 9.43e-01 4.75e+01 angle pdb=" C THR G 99 " pdb=" N PRO G 100 " pdb=" CA PRO G 100 " ideal model delta sigma weight residual 119.78 126.87 -7.09 1.03e+00 9.43e-01 4.73e+01 ... (remaining 28531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 12365 15.83 - 31.66: 343 31.66 - 47.49: 60 47.49 - 63.32: 24 63.32 - 79.15: 36 Dihedral angle restraints: 12828 sinusoidal: 5088 harmonic: 7740 Sorted by residual: dihedral pdb=" C LEU T 99 " pdb=" N LEU T 99 " pdb=" CA LEU T 99 " pdb=" CB LEU T 99 " ideal model delta harmonic sigma weight residual -122.60 -114.32 -8.28 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C LEU D 99 " pdb=" N LEU D 99 " pdb=" CA LEU D 99 " pdb=" CB LEU D 99 " ideal model delta harmonic sigma weight residual -122.60 -114.33 -8.27 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" C LEU F 99 " pdb=" N LEU F 99 " pdb=" CA LEU F 99 " pdb=" CB LEU F 99 " ideal model delta harmonic sigma weight residual -122.60 -114.34 -8.26 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 12825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1797 0.069 - 0.139: 1059 0.139 - 0.208: 564 0.208 - 0.278: 84 0.278 - 0.347: 12 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CA PHE D 65 " pdb=" N PHE D 65 " pdb=" C PHE D 65 " pdb=" CB PHE D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PHE L 65 " pdb=" N PHE L 65 " pdb=" C PHE L 65 " pdb=" CB PHE L 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PHE R 65 " pdb=" N PHE R 65 " pdb=" C PHE R 65 " pdb=" CB PHE R 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 3513 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 50 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C VAL K 50 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL K 50 " 0.015 2.00e-02 2.50e+03 pdb=" N THR K 51 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 50 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.59e+00 pdb=" C VAL I 50 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL I 50 " -0.015 2.00e-02 2.50e+03 pdb=" N THR I 51 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL V 50 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C VAL V 50 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL V 50 " -0.015 2.00e-02 2.50e+03 pdb=" N THR V 51 " -0.014 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 8066 2.87 - 3.38: 18735 3.38 - 3.89: 35040 3.89 - 4.39: 41795 4.39 - 4.90: 69355 Nonbonded interactions: 172991 Sorted by model distance: nonbonded pdb=" N ASP S 53 " pdb=" OD1 ASP S 53 " model vdw 2.365 2.520 nonbonded pdb=" N ASP C 53 " pdb=" OD1 ASP C 53 " model vdw 2.365 2.520 nonbonded pdb=" N ASP Q 53 " pdb=" OD1 ASP Q 53 " model vdw 2.365 2.520 nonbonded pdb=" N ASP I 53 " pdb=" OD1 ASP I 53 " model vdw 2.365 2.520 nonbonded pdb=" N ASP E 53 " pdb=" OD1 ASP E 53 " model vdw 2.365 2.520 ... (remaining 172986 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 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.060 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: 31.170 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 53.860 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.025 0.116 20904 Z= 1.693 Angle : 1.676 9.251 28536 Z= 1.148 Chirality : 0.102 0.347 3516 Planarity : 0.008 0.040 3660 Dihedral : 9.891 79.155 7788 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2616 helix: -0.47 (0.15), residues: 888 sheet: 0.89 (0.18), residues: 840 loop : 1.83 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP H 98 HIS 0.005 0.001 HIS F 21 PHE 0.016 0.007 PHE M 58 TYR 0.032 0.006 TYR L 78 ARG 0.008 0.001 ARG N 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 608 time to evaluate : 2.214 Fit side-chains revert: symmetry clash REVERT: D 42 TYR cc_start: 0.9348 (p90) cc_final: 0.9098 (p90) REVERT: G 26 GLU cc_start: 0.8689 (tt0) cc_final: 0.8485 (tt0) REVERT: K 70 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7946 (mmt180) REVERT: O 26 GLU cc_start: 0.8595 (tt0) cc_final: 0.8370 (tt0) REVERT: O 75 SER cc_start: 0.8974 (p) cc_final: 0.8573 (m) REVERT: V 114 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7774 (ptm160) REVERT: X 68 MET cc_start: 0.9107 (mtp) cc_final: 0.8683 (mtm) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 2.2831 time to fit residues: 1493.5195 Evaluate side-chains 390 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN H 21 HIS ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 ASN ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 HIS ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 HIS T 52 HIS ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 HIS W 33 ASN ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 52 HIS ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 20904 Z= 0.286 Angle : 0.594 8.579 28536 Z= 0.308 Chirality : 0.050 0.161 3516 Planarity : 0.006 0.032 3660 Dihedral : 4.251 14.162 2892 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.93 % Allowed : 11.83 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2616 helix: 1.42 (0.17), residues: 816 sheet: 0.58 (0.17), residues: 804 loop : 1.05 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 98 HIS 0.005 0.001 HIS J 21 PHE 0.014 0.002 PHE K 58 TYR 0.010 0.002 TYR O 108 ARG 0.005 0.001 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 504 time to evaluate : 2.390 Fit side-chains REVERT: A 53 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8221 (mm-30) REVERT: C 38 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7859 (OUTLIER) REVERT: C 103 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.8016 (mtp180) REVERT: E 40 TYR cc_start: 0.8851 (m-10) cc_final: 0.8632 (m-80) REVERT: F 67 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8531 (mppt) REVERT: F 69 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8630 (mtmm) REVERT: G 26 GLU cc_start: 0.8845 (tt0) cc_final: 0.8364 (tt0) REVERT: G 38 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7972 (mm-40) REVERT: I 77 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7497 (ttt-90) REVERT: J 53 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: K 70 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7927 (mmt180) REVERT: L 94 GLU cc_start: 0.8030 (mp0) cc_final: 0.7588 (mp0) REVERT: N 70 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: O 26 GLU cc_start: 0.8813 (tt0) cc_final: 0.8321 (tt0) REVERT: O 77 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7333 (ttt-90) REVERT: P 42 TYR cc_start: 0.9250 (p90) cc_final: 0.8799 (p90) REVERT: P 70 GLU cc_start: 0.7673 (mp0) cc_final: 0.7378 (mp0) REVERT: Q 69 HIS cc_start: 0.8291 (m-70) cc_final: 0.8067 (m-70) REVERT: Q 70 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7848 (mtt-85) REVERT: T 18 LYS cc_start: 0.8568 (tptt) cc_final: 0.8329 (ttmt) REVERT: V 75 SER cc_start: 0.9069 (p) cc_final: 0.8759 (m) REVERT: V 114 ARG cc_start: 0.8015 (ptp-170) cc_final: 0.7738 (ptm160) REVERT: W 70 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: W 71 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.9091 (tpt90) REVERT: W 94 GLU cc_start: 0.8079 (mp0) cc_final: 0.7711 (mp0) outliers start: 43 outliers final: 6 residues processed: 516 average time/residue: 2.0468 time to fit residues: 1144.2793 Evaluate side-chains 434 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 420 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 33 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 204 optimal weight: 0.0020 chunk 227 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20904 Z= 0.251 Angle : 0.528 8.647 28536 Z= 0.272 Chirality : 0.048 0.150 3516 Planarity : 0.005 0.034 3660 Dihedral : 3.899 12.691 2892 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.05 % Allowed : 14.29 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2616 helix: 1.44 (0.17), residues: 816 sheet: 0.36 (0.18), residues: 696 loop : 0.94 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 98 HIS 0.004 0.001 HIS H 21 PHE 0.011 0.002 PHE V 58 TYR 0.012 0.002 TYR L 95 ARG 0.008 0.000 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 416 time to evaluate : 2.469 Fit side-chains REVERT: A 70 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: F 67 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8664 (mtmm) REVERT: F 69 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8559 (mtmm) REVERT: G 38 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8095 (mm-40) REVERT: K 70 ARG cc_start: 0.8259 (mtt90) cc_final: 0.8032 (mmt180) REVERT: K 114 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7614 (ptp-110) REVERT: N 59 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8943 (mmtm) REVERT: N 70 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: O 26 GLU cc_start: 0.8813 (tt0) cc_final: 0.8351 (tt0) REVERT: O 77 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7490 (ttt-90) REVERT: P 42 TYR cc_start: 0.9251 (p90) cc_final: 0.9035 (p90) REVERT: P 53 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: Q 70 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.8063 (mtt-85) REVERT: R 70 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: V 53 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8497 (p0) REVERT: V 78 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7501 (tp30) REVERT: W 70 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: W 71 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8720 (tpt-90) outliers start: 68 outliers final: 14 residues processed: 436 average time/residue: 2.1509 time to fit residues: 1015.2411 Evaluate side-chains 423 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 397 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 243 optimal weight: 0.0970 chunk 120 optimal weight: 0.7980 chunk 218 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20904 Z= 0.269 Angle : 0.528 7.936 28536 Z= 0.269 Chirality : 0.048 0.147 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.912 13.165 2892 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.78 % Allowed : 15.23 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2616 helix: 1.38 (0.17), residues: 816 sheet: 0.12 (0.16), residues: 900 loop : 1.34 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 98 HIS 0.003 0.001 HIS J 21 PHE 0.010 0.002 PHE D 65 TYR 0.013 0.002 TYR T 42 ARG 0.006 0.000 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 406 time to evaluate : 2.843 Fit side-chains REVERT: A 70 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: D 70 GLU cc_start: 0.7727 (mp0) cc_final: 0.7424 (mp0) REVERT: F 69 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8592 (mtmm) REVERT: G 38 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8180 (mm-40) REVERT: K 114 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7597 (ptp-110) REVERT: M 30 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8821 (mmmt) REVERT: N 70 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: O 77 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7485 (ttt-90) REVERT: P 42 TYR cc_start: 0.9238 (p90) cc_final: 0.9034 (p90) REVERT: P 53 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: P 70 GLU cc_start: 0.7674 (mp0) cc_final: 0.7459 (mp0) REVERT: Q 39 SER cc_start: 0.8355 (t) cc_final: 0.7946 (p) REVERT: Q 77 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7873 (ttt-90) REVERT: R 70 GLU cc_start: 0.7711 (mp0) cc_final: 0.7487 (mp0) REVERT: V 53 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8505 (p0) REVERT: V 78 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7560 (tp30) REVERT: W 70 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: W 71 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8734 (tpt-90) outliers start: 62 outliers final: 22 residues processed: 426 average time/residue: 2.1831 time to fit residues: 1003.0796 Evaluate side-chains 433 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 399 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 218 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 HIS ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20904 Z= 0.292 Angle : 0.537 9.646 28536 Z= 0.272 Chirality : 0.049 0.149 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.942 13.016 2892 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 3.27 % Allowed : 15.14 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2616 helix: 1.32 (0.17), residues: 816 sheet: 0.29 (0.19), residues: 672 loop : 0.67 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 95 HIS 0.004 0.001 HIS N 21 PHE 0.010 0.002 PHE V 58 TYR 0.014 0.002 TYR T 42 ARG 0.007 0.000 ARG Q 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 397 time to evaluate : 2.458 Fit side-chains REVERT: B 103 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.8010 (mtm110) REVERT: A 70 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 70 GLU cc_start: 0.7784 (mp0) cc_final: 0.7572 (mp0) REVERT: F 69 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8527 (mtmm) REVERT: G 38 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7777 (mp10) REVERT: I 111 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8118 (mm-30) REVERT: K 64 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7803 (mtt180) REVERT: K 114 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7644 (ptp-110) REVERT: L 70 GLU cc_start: 0.7777 (mp0) cc_final: 0.7561 (mp0) REVERT: M 30 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8836 (mmmt) REVERT: N 59 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8802 (mmtm) REVERT: N 70 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: O 77 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7541 (ttt-90) REVERT: P 53 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: P 70 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: Q 77 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7916 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7428 (ptp-110) REVERT: R 70 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: S 114 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7802 (mtm-85) REVERT: T 43 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8578 (ttt180) REVERT: V 53 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8504 (p0) REVERT: W 70 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: W 71 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8743 (tpt-90) REVERT: Y 18 LYS cc_start: 0.8893 (tptt) cc_final: 0.8620 (ttpt) outliers start: 73 outliers final: 27 residues processed: 416 average time/residue: 2.1550 time to fit residues: 967.4232 Evaluate side-chains 437 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 392 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 40 SER Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 43 ARG Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.0070 chunk 243 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 HIS ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20904 Z= 0.212 Angle : 0.497 8.580 28536 Z= 0.252 Chirality : 0.047 0.150 3516 Planarity : 0.005 0.033 3660 Dihedral : 3.791 12.610 2892 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.64 % Allowed : 15.86 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2616 helix: 1.43 (0.17), residues: 816 sheet: 0.16 (0.16), residues: 864 loop : 1.12 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 95 HIS 0.003 0.001 HIS N 21 PHE 0.010 0.002 PHE J 65 TYR 0.014 0.001 TYR T 42 ARG 0.006 0.000 ARG V 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 399 time to evaluate : 2.383 Fit side-chains REVERT: B 103 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7960 (mtm110) REVERT: A 70 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: F 69 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8445 (mtmm) REVERT: G 114 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7978 (ptp-110) REVERT: G 115 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8823 (pp) REVERT: J 53 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: K 114 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7634 (ptp-110) REVERT: M 30 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8834 (mmmt) REVERT: M 114 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7827 (ptp-110) REVERT: N 59 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8798 (mmtm) REVERT: N 70 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: O 64 ARG cc_start: 0.8361 (mmt180) cc_final: 0.8128 (mmt90) REVERT: O 77 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7491 (ttt-90) REVERT: P 53 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: P 70 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: Q 77 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7845 (ttt-90) REVERT: R 42 TYR cc_start: 0.9283 (p90) cc_final: 0.9063 (p90) REVERT: R 70 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: S 114 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7796 (mtm-85) REVERT: T 43 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8574 (ttt180) REVERT: W 70 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: W 71 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8700 (tpt-90) REVERT: Y 18 LYS cc_start: 0.8838 (tptt) cc_final: 0.8602 (ttpt) outliers start: 59 outliers final: 14 residues processed: 415 average time/residue: 2.1714 time to fit residues: 971.8206 Evaluate side-chains 421 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 388 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain T residue 43 ARG Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20904 Z= 0.310 Angle : 0.543 8.476 28536 Z= 0.275 Chirality : 0.049 0.149 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.930 12.845 2892 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.91 % Allowed : 15.86 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.16), residues: 2616 helix: 1.30 (0.17), residues: 816 sheet: 0.23 (0.19), residues: 672 loop : 0.60 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 98 HIS 0.004 0.001 HIS N 21 PHE 0.011 0.002 PHE D 65 TYR 0.015 0.002 TYR T 42 ARG 0.007 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 402 time to evaluate : 2.605 Fit side-chains REVERT: B 103 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7936 (mtm110) REVERT: A 70 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: D 70 GLU cc_start: 0.7751 (mp0) cc_final: 0.7421 (mp0) REVERT: F 69 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8453 (mtmm) REVERT: G 114 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.8024 (ptp-110) REVERT: G 115 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8952 (pp) REVERT: J 53 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: K 64 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7819 (mtt180) REVERT: K 114 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7591 (ptp-110) REVERT: L 70 GLU cc_start: 0.7868 (mp0) cc_final: 0.7643 (mp0) REVERT: M 30 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8837 (mmmt) REVERT: M 114 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7899 (ptp-110) REVERT: N 59 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8785 (mmtm) REVERT: N 70 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: O 64 ARG cc_start: 0.8331 (mmt180) cc_final: 0.8123 (mmt90) REVERT: O 77 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7586 (ttt-90) REVERT: P 53 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: Q 77 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7897 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7447 (ptp-110) REVERT: R 70 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: S 114 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7808 (mtm-85) REVERT: T 43 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8631 (ttt180) REVERT: W 70 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: W 71 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8731 (tpt-90) REVERT: Y 18 LYS cc_start: 0.8841 (tptt) cc_final: 0.8571 (ttpt) outliers start: 65 outliers final: 25 residues processed: 424 average time/residue: 2.2077 time to fit residues: 1011.8899 Evaluate side-chains 444 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 400 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 43 ARG Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 220 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20904 Z= 0.284 Angle : 0.533 8.247 28536 Z= 0.269 Chirality : 0.048 0.149 3516 Planarity : 0.005 0.034 3660 Dihedral : 3.917 12.850 2892 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 16.04 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 2616 helix: 1.31 (0.17), residues: 816 sheet: 0.22 (0.19), residues: 672 loop : 0.56 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 98 HIS 0.004 0.001 HIS N 21 PHE 0.010 0.002 PHE E 48 TYR 0.015 0.002 TYR T 42 ARG 0.007 0.000 ARG V 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 403 time to evaluate : 2.489 Fit side-chains REVERT: B 68 MET cc_start: 0.9105 (mtt) cc_final: 0.8832 (mtt) REVERT: B 103 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7938 (mtm110) REVERT: A 70 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: D 70 GLU cc_start: 0.7778 (mp0) cc_final: 0.7505 (mp0) REVERT: E 70 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7646 (mtp85) REVERT: F 69 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8475 (mtmm) REVERT: G 114 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.8002 (ptp-110) REVERT: G 115 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8937 (pp) REVERT: J 53 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: K 38 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: K 64 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7811 (mtt180) REVERT: K 114 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7635 (ptp-110) REVERT: L 70 GLU cc_start: 0.7834 (mp0) cc_final: 0.7615 (mp0) REVERT: M 114 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (ptp-110) REVERT: N 59 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8780 (mmtm) REVERT: N 70 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: O 64 ARG cc_start: 0.8357 (mmt180) cc_final: 0.8154 (mmt90) REVERT: O 77 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7463 (ttt-90) REVERT: P 53 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: P 70 GLU cc_start: 0.7711 (mp0) cc_final: 0.7499 (mp0) REVERT: Q 77 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7891 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7195 (ptp-110) REVERT: R 70 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: S 114 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7808 (mtm-85) REVERT: T 43 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8589 (ttt180) REVERT: V 38 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: W 70 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: W 71 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8726 (tpt-90) REVERT: Y 18 LYS cc_start: 0.8841 (tptt) cc_final: 0.8569 (ttpt) outliers start: 64 outliers final: 29 residues processed: 423 average time/residue: 2.1572 time to fit residues: 983.9567 Evaluate side-chains 448 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 398 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 114 ARG Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 43 ARG Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 38 GLN Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.2980 chunk 212 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 98 optimal weight: 0.0980 chunk 177 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20904 Z= 0.159 Angle : 0.475 10.134 28536 Z= 0.240 Chirality : 0.046 0.151 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.624 12.153 2892 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.79 % Allowed : 17.34 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2616 helix: 1.51 (0.18), residues: 816 sheet: 0.06 (0.16), residues: 888 loop : 1.14 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.003 0.001 HIS N 21 PHE 0.010 0.002 PHE Y 65 TYR 0.013 0.001 TYR T 42 ARG 0.008 0.000 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 415 time to evaluate : 2.358 Fit side-chains REVERT: B 103 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7943 (mtm110) REVERT: A 70 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: F 70 GLU cc_start: 0.7692 (mp0) cc_final: 0.7458 (mm-30) REVERT: G 115 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8921 (pp) REVERT: K 64 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7799 (mtt180) REVERT: K 114 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7586 (ptp-110) REVERT: M 114 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7792 (ptp-110) REVERT: N 59 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8759 (mmtm) REVERT: N 70 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: O 64 ARG cc_start: 0.8367 (mmt180) cc_final: 0.8155 (mmt90) REVERT: O 77 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7521 (ttt-90) REVERT: P 70 GLU cc_start: 0.7682 (mp0) cc_final: 0.7408 (mp0) REVERT: Q 30 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8827 (mmtp) REVERT: Q 77 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7799 (ttt-90) REVERT: R 70 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: V 38 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: V 114 ARG cc_start: 0.8132 (ptp-170) cc_final: 0.7853 (ptm160) REVERT: W 70 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: W 71 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8726 (tpt-90) REVERT: Y 18 LYS cc_start: 0.8776 (tptt) cc_final: 0.8569 (ttpt) outliers start: 40 outliers final: 17 residues processed: 430 average time/residue: 2.1136 time to fit residues: 983.1571 Evaluate side-chains 435 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 406 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 38 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 113 optimal weight: 0.0050 chunk 166 optimal weight: 0.9980 chunk 251 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20904 Z= 0.240 Angle : 0.520 10.008 28536 Z= 0.262 Chirality : 0.048 0.149 3516 Planarity : 0.005 0.039 3660 Dihedral : 3.732 12.314 2892 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.57 % Allowed : 18.19 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2616 helix: 1.42 (0.18), residues: 816 sheet: 0.02 (0.16), residues: 888 loop : 1.09 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 98 HIS 0.003 0.001 HIS R 21 PHE 0.011 0.002 PHE X 48 TYR 0.014 0.001 TYR T 42 ARG 0.009 0.001 ARG E 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 409 time to evaluate : 2.217 Fit side-chains REVERT: B 103 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7932 (mtm110) REVERT: A 70 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: F 70 GLU cc_start: 0.7738 (mp0) cc_final: 0.7486 (mm-30) REVERT: K 38 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: K 64 ARG cc_start: 0.8253 (mtt-85) cc_final: 0.7823 (mtt180) REVERT: K 114 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7561 (ptp-110) REVERT: M 114 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7834 (ptp-110) REVERT: N 59 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8790 (mmtm) REVERT: N 70 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: O 64 ARG cc_start: 0.8414 (mmt180) cc_final: 0.8197 (mmt90) REVERT: O 77 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7617 (ttt-90) REVERT: P 70 GLU cc_start: 0.7689 (mp0) cc_final: 0.7434 (mp0) REVERT: Q 77 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7862 (ttt-90) REVERT: R 70 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: V 30 LYS cc_start: 0.9155 (tppt) cc_final: 0.8890 (mmtm) REVERT: V 38 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: V 114 ARG cc_start: 0.8158 (ptp-170) cc_final: 0.7877 (ptm160) REVERT: W 70 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: W 71 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8707 (tpt-90) REVERT: Y 18 LYS cc_start: 0.8816 (tptt) cc_final: 0.8592 (ttpt) outliers start: 35 outliers final: 16 residues processed: 419 average time/residue: 2.2350 time to fit residues: 1010.0364 Evaluate side-chains 431 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 403 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain K residue 38 GLN Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain M residue 33 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 38 GLN Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 184 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** 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 = 0.2841 r_free = 0.2841 target = 0.087736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.072900 restraints weight = 26974.481| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.94 r_work: 0.2752 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20904 Z= 0.234 Angle : 0.519 9.859 28536 Z= 0.261 Chirality : 0.048 0.167 3516 Planarity : 0.005 0.040 3660 Dihedral : 3.766 12.548 2892 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.66 % Allowed : 18.28 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2616 helix: 1.38 (0.17), residues: 816 sheet: -0.02 (0.16), residues: 888 loop : 1.09 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 98 HIS 0.003 0.001 HIS N 21 PHE 0.009 0.002 PHE T 65 TYR 0.014 0.001 TYR T 42 ARG 0.010 0.000 ARG E 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13305.18 seconds wall clock time: 234 minutes 10.90 seconds (14050.90 seconds total)