Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 19:48:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/04_2023/7l85_23222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/04_2023/7l85_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_23222/04_2023/7l85_23222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/04_2023/7l85_23222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/04_2023/7l85_23222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l85_23222/04_2023/7l85_23222.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 10.88, per 1000 atoms: 0.53 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: 8.56 Conformation dependent library (CDL) restraints added in 3.1 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: 1.35 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: 6.95 Time building geometry restraints manager: 9.08 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: 6.700 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: 31.580 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 53.710 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.480 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.570 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 2.2823 time to fit residues: 1491.9739 Evaluate side-chains 387 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4221 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8980 chunk 147 optimal weight: 0.6980 chunk 228 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8679 moved from start: 0.3109 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= 0.296 Angle : 0.604 8.442 28536 Z= 0.315 Chirality : 0.050 0.163 3516 Planarity : 0.006 0.031 3660 Dihedral : 4.252 14.245 2892 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.97 % 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: 1.45 (0.16), residues: 2616 helix: 1.44 (0.17), residues: 816 sheet: 0.63 (0.17), residues: 804 loop : 1.09 (0.21), residues: 996 *********************** 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 544 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 500 time to evaluate : 2.499 Fit side-chains outliers start: 44 outliers final: 5 residues processed: 511 average time/residue: 2.1160 time to fit residues: 1170.0945 Evaluate side-chains 426 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 421 time to evaluate : 2.488 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 1.2945 time to fit residues: 10.5174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.0970 chunk 71 optimal weight: 0.1980 chunk 190 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 204 optimal weight: 0.0060 chunk 227 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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: 0.8655 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20904 Z= 0.158 Angle : 0.480 8.617 28536 Z= 0.249 Chirality : 0.046 0.148 3516 Planarity : 0.005 0.034 3660 Dihedral : 3.747 12.657 2892 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.37 % 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: 1.58 (0.16), residues: 2616 helix: 1.61 (0.17), residues: 816 sheet: 0.72 (0.17), residues: 756 loop : 1.07 (0.20), residues: 1044 *********************** 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 478 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 425 time to evaluate : 2.480 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 8 residues processed: 441 average time/residue: 2.1216 time to fit residues: 1013.9665 Evaluate side-chains 406 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 398 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 6 average time/residue: 1.0470 time to fit residues: 10.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 243 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 218 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8719 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 20904 Z= 0.309 Angle : 0.553 10.154 28536 Z= 0.281 Chirality : 0.049 0.147 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.933 12.892 2892 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.42 % 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: 1.26 (0.16), residues: 2616 helix: 1.41 (0.17), residues: 816 sheet: 0.49 (0.17), residues: 756 loop : 0.88 (0.20), residues: 1044 *********************** 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 461 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 407 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 19 residues processed: 424 average time/residue: 2.1802 time to fit residues: 998.0329 Evaluate side-chains 418 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 399 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 4 residues processed: 15 average time/residue: 0.9890 time to fit residues: 20.3442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 3 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 0.0970 chunk 168 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.8713 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 20904 Z= 0.255 Angle : 0.518 8.995 28536 Z= 0.263 Chirality : 0.048 0.146 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.865 12.655 2892 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.93 % 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: 1.07 (0.16), residues: 2616 helix: 1.37 (0.17), residues: 816 sheet: 0.06 (0.17), residues: 780 loop : 0.96 (0.20), residues: 1020 *********************** 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 448 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 405 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 16 residues processed: 415 average time/residue: 2.2130 time to fit residues: 992.0829 Evaluate side-chains 419 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 403 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 4 residues processed: 12 average time/residue: 1.0395 time to fit residues: 17.3226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.2980 chunk 219 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 52 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4018 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= 0.206 Angle : 0.498 9.227 28536 Z= 0.253 Chirality : 0.047 0.145 3516 Planarity : 0.005 0.036 3660 Dihedral : 3.757 12.285 2892 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 1.97 % 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: 1.23 (0.16), residues: 2616 helix: 1.43 (0.18), residues: 816 sheet: 0.18 (0.16), residues: 864 loop : 1.18 (0.21), residues: 936 *********************** 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 447 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 403 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 417 average time/residue: 2.2374 time to fit residues: 1004.6890 Evaluate side-chains 413 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 391 time to evaluate : 2.552 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 8 residues processed: 14 average time/residue: 0.8653 time to fit residues: 18.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** 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: 0.8733 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 20904 Z= 0.326 Angle : 0.555 9.233 28536 Z= 0.281 Chirality : 0.049 0.147 3516 Planarity : 0.005 0.037 3660 Dihedral : 3.948 12.798 2892 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 2.37 % 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: 1.01 (0.16), residues: 2616 helix: 1.25 (0.17), residues: 816 sheet: 0.10 (0.18), residues: 744 loop : 0.89 (0.19), residues: 1056 *********************** 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 457 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 404 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 418 average time/residue: 2.3128 time to fit residues: 1044.9954 Evaluate side-chains 421 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 399 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 7 residues processed: 15 average time/residue: 1.1501 time to fit residues: 23.2553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 154 optimal weight: 0.0170 chunk 165 optimal weight: 0.5980 chunk 120 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** 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: 0.8703 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 20904 Z= 0.205 Angle : 0.503 8.544 28536 Z= 0.256 Chirality : 0.047 0.148 3516 Planarity : 0.005 0.039 3660 Dihedral : 3.774 12.462 2892 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2616 helix: 1.34 (0.18), residues: 816 sheet: -0.03 (0.16), residues: 888 loop : 1.12 (0.21), residues: 912 *********************** 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 431 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 401 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 414 average time/residue: 2.2588 time to fit residues: 1008.7732 Evaluate side-chains 407 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 389 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 9 average time/residue: 1.0224 time to fit residues: 14.1061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.6980 chunk 212 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 98 optimal weight: 0.2980 chunk 177 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 225 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 21 HIS ** 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: 0.8713 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20904 Z= 0.248 Angle : 0.529 9.838 28536 Z= 0.269 Chirality : 0.048 0.156 3516 Planarity : 0.005 0.039 3660 Dihedral : 3.813 12.548 2892 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 1.34 % 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: 0.99 (0.16), residues: 2616 helix: 1.25 (0.18), residues: 816 sheet: 0.04 (0.16), residues: 864 loop : 1.04 (0.21), residues: 936 *********************** 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 431 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 401 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 414 average time/residue: 2.2060 time to fit residues: 986.2468 Evaluate side-chains 414 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 399 time to evaluate : 2.593 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 1.0963 time to fit residues: 11.0540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 166 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8707 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 20904 Z= 0.231 Angle : 0.522 9.601 28536 Z= 0.266 Chirality : 0.048 0.182 3516 Planarity : 0.005 0.039 3660 Dihedral : 3.792 12.463 2892 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.16), residues: 2616 helix: 1.25 (0.18), residues: 816 sheet: 0.02 (0.16), residues: 864 loop : 1.05 (0.21), residues: 936 ********************** 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 421 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 400 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 410 average time/residue: 2.2464 time to fit residues: 996.1295 Evaluate side-chains 416 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 400 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 9 residues processed: 7 average time/residue: 0.7596 time to fit residues: 9.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 175 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.086464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.071539 restraints weight = 27110.412| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.94 r_work: 0.2654 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20904 Z= 0.308 Angle : 0.552 9.816 28536 Z= 0.279 Chirality : 0.049 0.169 3516 Planarity : 0.005 0.040 3660 Dihedral : 3.927 12.805 2892 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.08 % 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: 0.92 (0.16), residues: 2616 helix: 1.24 (0.17), residues: 816 sheet: -0.02 (0.16), residues: 864 loop : 0.98 (0.21), residues: 936 =============================================================================== Job complete usr+sys time: 13224.42 seconds wall clock time: 232 minutes 25.65 seconds (13945.65 seconds total)