Starting phenix.real_space_refine on Sun Mar 17 20:06:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/03_2024/6nav_0397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/03_2024/6nav_0397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/03_2024/6nav_0397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/03_2024/6nav_0397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/03_2024/6nav_0397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/03_2024/6nav_0397.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.007 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: 3 Type Number sf(0) Gaussians C 11781 2.51 5 N 3045 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18711 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "C" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "D" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "E" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "G" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "I" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "J" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "K" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "L" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "O" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "P" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "Q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "R" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "S" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "T" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "U" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Time building chain proxies: 9.95, per 1000 atoms: 0.53 Number of scatterers: 18711 At special positions: 0 Unit cell: (93.8, 93.8, 197.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3885 8.00 N 3045 7.00 C 11781 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: 6.53 Conformation dependent library (CDL) restraints added in 3.6 seconds 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 63 sheets defined 29.8% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 4.141A pdb=" N ALA A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 104' Processing helix chain 'B' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 104' Processing helix chain 'C' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 removed outlier: 4.412A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 104' Processing helix chain 'D' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 16 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 104' Processing helix chain 'E' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU E 8 " --> pdb=" O ALA E 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 16 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 104' Processing helix chain 'F' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 15 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR F 33 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 104' Processing helix chain 'G' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 15 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 104' Processing helix chain 'H' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU H 8 " --> pdb=" O ALA H 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL H 15 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 16 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 removed outlier: 4.412A pdb=" N LEU H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 99 through 104' Processing helix chain 'I' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA I 7 " --> pdb=" O GLY I 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL I 15 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE I 16 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU I 103 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 104 " --> pdb=" O SER I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 104' Processing helix chain 'J' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA J 7 " --> pdb=" O GLY J 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU J 8 " --> pdb=" O ALA J 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL J 15 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR J 33 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU J 103 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN J 104 " --> pdb=" O SER J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 99 through 104' Processing helix chain 'K' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU K 8 " --> pdb=" O ALA K 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL K 15 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE K 16 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 99 through 104' Processing helix chain 'L' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU L 8 " --> pdb=" O ALA L 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL L 15 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE L 16 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU L 103 " --> pdb=" O SER L 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN L 104 " --> pdb=" O SER L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 104' Processing helix chain 'M' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL M 15 " --> pdb=" O VAL M 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE M 16 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU M 103 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN M 104 " --> pdb=" O SER M 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 99 through 104' Processing helix chain 'N' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA N 7 " --> pdb=" O GLY N 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE N 16 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 104 removed outlier: 4.412A pdb=" N LEU N 103 " --> pdb=" O SER N 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN N 104 " --> pdb=" O SER N 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 104' Processing helix chain 'O' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU O 8 " --> pdb=" O ALA O 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE O 16 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU O 103 " --> pdb=" O SER O 99 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN O 104 " --> pdb=" O SER O 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 104' Processing helix chain 'P' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU P 8 " --> pdb=" O ALA P 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL P 15 " --> pdb=" O VAL P 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE P 16 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY P 34 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU P 103 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN P 104 " --> pdb=" O SER P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 99 through 104' Processing helix chain 'Q' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU Q 8 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE Q 16 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU Q 103 " --> pdb=" O SER Q 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Q 104 " --> pdb=" O SER Q 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 99 through 104' Processing helix chain 'R' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA R 7 " --> pdb=" O GLY R 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU R 8 " --> pdb=" O ALA R 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL R 15 " --> pdb=" O VAL R 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE R 16 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN R 104 " --> pdb=" O SER R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 99 through 104' Processing helix chain 'S' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA S 7 " --> pdb=" O GLY S 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU S 8 " --> pdb=" O ALA S 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL S 15 " --> pdb=" O VAL S 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 16 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR S 33 " --> pdb=" O PHE S 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU S 103 " --> pdb=" O SER S 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN S 104 " --> pdb=" O SER S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 99 through 104' Processing helix chain 'T' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA T 7 " --> pdb=" O GLY T 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU T 8 " --> pdb=" O ALA T 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL T 15 " --> pdb=" O VAL T 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR T 33 " --> pdb=" O PHE T 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN T 104 " --> pdb=" O SER T 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 99 through 104' Processing helix chain 'U' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA U 7 " --> pdb=" O GLY U 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU U 8 " --> pdb=" O ALA U 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL U 15 " --> pdb=" O VAL U 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE U 16 " --> pdb=" O ILE U 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU U 103 " --> pdb=" O SER U 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN U 104 " --> pdb=" O SER U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 99 through 104' Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY A 68 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 45 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 52 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY B 68 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 45 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR B 52 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 40 Processing sheet with id=AA8, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY C 68 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 45 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 52 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 40 Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 77 Processing sheet with id=AB3, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY D 68 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 45 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR D 52 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AB5, first strand: chain 'E' and resid 74 through 77 Processing sheet with id=AB6, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY E 68 " --> pdb=" O GLN E 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 45 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR E 52 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 40 Processing sheet with id=AB8, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AB9, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY F 68 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 45 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR F 52 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AC2, first strand: chain 'G' and resid 74 through 77 Processing sheet with id=AC3, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY G 68 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 45 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR G 52 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 38 through 40 Processing sheet with id=AC5, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AC6, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY H 68 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR H 45 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR H 52 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 38 through 40 Processing sheet with id=AC8, first strand: chain 'I' and resid 74 through 77 Processing sheet with id=AC9, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY I 68 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR I 45 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR I 52 " --> pdb=" O SER I 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 38 through 40 Processing sheet with id=AD2, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AD3, first strand: chain 'J' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY J 68 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR J 45 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR J 52 " --> pdb=" O SER J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AD5, first strand: chain 'K' and resid 74 through 77 Processing sheet with id=AD6, first strand: chain 'K' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY K 68 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR K 45 " --> pdb=" O LYS K 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR K 52 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 38 through 40 Processing sheet with id=AD8, first strand: chain 'L' and resid 74 through 77 Processing sheet with id=AD9, first strand: chain 'L' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY L 68 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR L 45 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR L 52 " --> pdb=" O SER L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 38 through 40 Processing sheet with id=AE2, first strand: chain 'M' and resid 74 through 77 Processing sheet with id=AE3, first strand: chain 'M' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY M 68 " --> pdb=" O GLN M 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR M 45 " --> pdb=" O LYS M 54 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR M 52 " --> pdb=" O SER M 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 38 through 40 Processing sheet with id=AE5, first strand: chain 'N' and resid 74 through 77 Processing sheet with id=AE6, first strand: chain 'N' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY N 68 " --> pdb=" O GLN N 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR N 45 " --> pdb=" O LYS N 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR N 52 " --> pdb=" O SER N 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 38 through 40 Processing sheet with id=AE8, first strand: chain 'O' and resid 74 through 77 Processing sheet with id=AE9, first strand: chain 'O' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY O 68 " --> pdb=" O GLN O 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR O 45 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR O 52 " --> pdb=" O SER O 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 38 through 40 Processing sheet with id=AF2, first strand: chain 'P' and resid 74 through 77 Processing sheet with id=AF3, first strand: chain 'P' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY P 68 " --> pdb=" O GLN P 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR P 45 " --> pdb=" O LYS P 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR P 52 " --> pdb=" O SER P 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id=AF5, first strand: chain 'Q' and resid 74 through 77 Processing sheet with id=AF6, first strand: chain 'Q' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY Q 68 " --> pdb=" O GLN Q 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR Q 45 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR Q 52 " --> pdb=" O SER Q 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 38 through 40 Processing sheet with id=AF8, first strand: chain 'R' and resid 74 through 77 Processing sheet with id=AF9, first strand: chain 'R' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY R 68 " --> pdb=" O GLN R 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR R 45 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR R 52 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 38 through 40 Processing sheet with id=AG2, first strand: chain 'S' and resid 74 through 77 Processing sheet with id=AG3, first strand: chain 'S' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY S 68 " --> pdb=" O GLN S 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 45 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR S 52 " --> pdb=" O SER S 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 38 through 40 Processing sheet with id=AG5, first strand: chain 'T' and resid 74 through 77 Processing sheet with id=AG6, first strand: chain 'T' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY T 68 " --> pdb=" O GLN T 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR T 45 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR T 52 " --> pdb=" O SER T 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 38 through 40 Processing sheet with id=AG8, first strand: chain 'U' and resid 74 through 77 Processing sheet with id=AG9, first strand: chain 'U' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY U 68 " --> pdb=" O GLN U 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR U 45 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR U 52 " --> pdb=" O SER U 47 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3027 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: 6.06 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3024 1.29 - 1.36: 2982 1.36 - 1.42: 1050 1.42 - 1.49: 3255 1.49 - 1.56: 8484 Bond restraints: 18795 Sorted by residual: bond pdb=" CA THR F 90 " pdb=" CB THR F 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.04e+00 bond pdb=" CA THR T 90 " pdb=" CB THR T 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" CA THR L 90 " pdb=" CB THR L 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" CA THR H 90 " pdb=" CB THR H 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" CA THR O 90 " pdb=" CB THR O 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.00e+00 ... (remaining 18790 not shown) Histogram of bond angle deviations from ideal: 104.77 - 109.46: 2199 109.46 - 114.16: 10317 114.16 - 118.86: 3618 118.86 - 123.56: 9320 123.56 - 128.26: 250 Bond angle restraints: 25704 Sorted by residual: angle pdb=" C SER R 89 " pdb=" N THR R 90 " pdb=" CA THR R 90 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C SER E 89 " pdb=" N THR E 90 " pdb=" CA THR E 90 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C SER H 89 " pdb=" N THR H 90 " pdb=" CA THR H 90 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C SER C 89 " pdb=" N THR C 90 " pdb=" CA THR C 90 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C SER T 89 " pdb=" N THR T 90 " pdb=" CA THR T 90 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 ... (remaining 25699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 10227 11.10 - 22.21: 441 22.21 - 33.31: 126 33.31 - 44.42: 42 44.42 - 55.52: 21 Dihedral angle restraints: 10857 sinusoidal: 3318 harmonic: 7539 Sorted by residual: dihedral pdb=" CA GLN Q 88 " pdb=" C GLN Q 88 " pdb=" N SER Q 89 " pdb=" CA SER Q 89 " ideal model delta harmonic sigma weight residual -180.00 -124.48 -55.52 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLN O 88 " pdb=" C GLN O 88 " pdb=" N SER O 89 " pdb=" CA SER O 89 " ideal model delta harmonic sigma weight residual -180.00 -124.50 -55.50 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLN I 88 " pdb=" C GLN I 88 " pdb=" N SER I 89 " pdb=" CA SER I 89 " ideal model delta harmonic sigma weight residual -180.00 -124.51 -55.49 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 10854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2486 0.046 - 0.091: 840 0.091 - 0.137: 307 0.137 - 0.182: 42 0.182 - 0.228: 21 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CB ILE C 71 " pdb=" CA ILE C 71 " pdb=" CG1 ILE C 71 " pdb=" CG2 ILE C 71 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE N 71 " pdb=" CA ILE N 71 " pdb=" CG1 ILE N 71 " pdb=" CG2 ILE N 71 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3693 not shown) Planarity restraints: 3108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 89 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C SER E 89 " 0.029 2.00e-02 2.50e+03 pdb=" O SER E 89 " -0.011 2.00e-02 2.50e+03 pdb=" N THR E 90 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 89 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C SER L 89 " -0.029 2.00e-02 2.50e+03 pdb=" O SER L 89 " 0.011 2.00e-02 2.50e+03 pdb=" N THR L 90 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN N 88 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C GLN N 88 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN N 88 " 0.011 2.00e-02 2.50e+03 pdb=" N SER N 89 " 0.010 2.00e-02 2.50e+03 ... (remaining 3105 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3660 2.78 - 3.31: 17111 3.31 - 3.84: 30074 3.84 - 4.37: 31846 4.37 - 4.90: 61367 Nonbonded interactions: 144058 Sorted by model distance: nonbonded pdb=" OG SER M 14 " pdb=" OG1 THR S 6 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR L 6 " pdb=" OG SER R 14 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 14 " pdb=" OG1 THR E 6 " model vdw 2.245 2.440 nonbonded pdb=" OG SER I 14 " pdb=" OG1 THR O 6 " model vdw 2.245 2.440 nonbonded pdb=" OG SER K 14 " pdb=" OG1 THR Q 6 " model vdw 2.245 2.440 ... (remaining 144053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.010 Extract box with map and model: 12.220 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.440 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.005 0.036 18795 Z= 0.337 Angle : 0.823 7.543 25704 Z= 0.454 Chirality : 0.055 0.228 3696 Planarity : 0.005 0.017 3108 Dihedral : 8.772 55.521 6069 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.14), residues: 2709 helix: -1.01 (0.17), residues: 651 sheet: -2.40 (0.18), residues: 714 loop : -2.14 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.004 PHE E 29 TYR 0.021 0.005 TYR P 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.142 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8673 (pp30) cc_final: 0.8123 (pp30) REVERT: A 81 GLN cc_start: 0.7381 (mp10) cc_final: 0.6621 (tp40) REVERT: B 81 GLN cc_start: 0.7138 (mp10) cc_final: 0.6811 (tp-100) REVERT: C 59 ASN cc_start: 0.8729 (t0) cc_final: 0.8431 (t0) REVERT: C 81 GLN cc_start: 0.7452 (mp10) cc_final: 0.7013 (mp10) REVERT: C 121 GLN cc_start: 0.8718 (tt0) cc_final: 0.8429 (tt0) REVERT: C 124 THR cc_start: 0.8838 (p) cc_final: 0.8567 (p) REVERT: D 60 THR cc_start: 0.8460 (p) cc_final: 0.8196 (t) REVERT: E 40 GLN cc_start: 0.8286 (tt0) cc_final: 0.7629 (tt0) REVERT: E 59 ASN cc_start: 0.8666 (t0) cc_final: 0.8420 (t0) REVERT: F 59 ASN cc_start: 0.8839 (t0) cc_final: 0.8547 (t0) REVERT: F 81 GLN cc_start: 0.7283 (mp10) cc_final: 0.7082 (mm-40) REVERT: F 124 THR cc_start: 0.8608 (p) cc_final: 0.8365 (p) REVERT: G 81 GLN cc_start: 0.7311 (mp10) cc_final: 0.6839 (mp10) REVERT: G 124 THR cc_start: 0.8641 (p) cc_final: 0.8423 (p) REVERT: H 21 VAL cc_start: 0.9122 (t) cc_final: 0.8883 (p) REVERT: H 40 GLN cc_start: 0.8464 (tt0) cc_final: 0.7931 (tt0) REVERT: H 59 ASN cc_start: 0.8731 (t0) cc_final: 0.8332 (t0) REVERT: H 81 GLN cc_start: 0.6837 (mp10) cc_final: 0.6614 (mm-40) REVERT: I 81 GLN cc_start: 0.7633 (mp10) cc_final: 0.6936 (mm-40) REVERT: J 59 ASN cc_start: 0.8847 (t0) cc_final: 0.8575 (t0) REVERT: J 81 GLN cc_start: 0.6674 (mp10) cc_final: 0.6326 (tp-100) REVERT: J 124 THR cc_start: 0.8597 (p) cc_final: 0.8326 (p) REVERT: K 81 GLN cc_start: 0.7540 (mp10) cc_final: 0.7050 (tp-100) REVERT: L 29 PHE cc_start: 0.7751 (t80) cc_final: 0.7509 (t80) REVERT: L 59 ASN cc_start: 0.8679 (t0) cc_final: 0.8130 (t0) REVERT: M 81 GLN cc_start: 0.7700 (mp10) cc_final: 0.6707 (tp40) REVERT: O 81 GLN cc_start: 0.7707 (mp10) cc_final: 0.7461 (mm-40) REVERT: P 29 PHE cc_start: 0.7632 (t80) cc_final: 0.7321 (t80) REVERT: P 40 GLN cc_start: 0.8844 (tt0) cc_final: 0.8344 (tt0) REVERT: Q 8 LEU cc_start: 0.7866 (tp) cc_final: 0.6309 (tp) REVERT: Q 81 GLN cc_start: 0.7781 (mp10) cc_final: 0.7339 (tp-100) REVERT: T 29 PHE cc_start: 0.7955 (t80) cc_final: 0.7680 (t80) REVERT: U 8 LEU cc_start: 0.7587 (tp) cc_final: 0.6081 (tp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2285 time to fit residues: 131.7021 Evaluate side-chains 137 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 247 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN D 121 GLN E 121 GLN F 121 GLN G 40 GLN G 88 GLN I 40 GLN I 88 GLN I 121 GLN K 40 GLN L 88 GLN M 59 ASN M 121 GLN O 88 GLN Q 40 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 GLN S 88 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18795 Z= 0.251 Angle : 0.559 8.575 25704 Z= 0.302 Chirality : 0.043 0.138 3696 Planarity : 0.002 0.013 3108 Dihedral : 5.210 39.486 2772 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -1.52 (0.16), residues: 2709 helix: 1.87 (0.20), residues: 651 sheet: -2.21 (0.17), residues: 819 loop : -1.68 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE A 29 TYR 0.021 0.003 TYR M 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.080 Fit side-chains REVERT: A 81 GLN cc_start: 0.7410 (mp10) cc_final: 0.6870 (mm-40) REVERT: C 81 GLN cc_start: 0.7493 (mp10) cc_final: 0.6982 (mp10) REVERT: C 121 GLN cc_start: 0.8719 (tt0) cc_final: 0.8445 (tt0) REVERT: D 35 GLN cc_start: 0.8801 (pp30) cc_final: 0.7846 (pp30) REVERT: D 59 ASN cc_start: 0.8789 (t0) cc_final: 0.8423 (t0) REVERT: D 60 THR cc_start: 0.8477 (p) cc_final: 0.8260 (t) REVERT: E 40 GLN cc_start: 0.8331 (tt0) cc_final: 0.7783 (tt0) REVERT: E 59 ASN cc_start: 0.8836 (t0) cc_final: 0.8482 (t0) REVERT: E 81 GLN cc_start: 0.7389 (mp10) cc_final: 0.6928 (mp10) REVERT: G 81 GLN cc_start: 0.7589 (mp10) cc_final: 0.6894 (mp10) REVERT: H 40 GLN cc_start: 0.8566 (tt0) cc_final: 0.7993 (tt0) REVERT: H 59 ASN cc_start: 0.8962 (t0) cc_final: 0.8665 (t0) REVERT: H 81 GLN cc_start: 0.6952 (mp10) cc_final: 0.6683 (mm-40) REVERT: I 81 GLN cc_start: 0.7486 (mp10) cc_final: 0.6805 (mm-40) REVERT: I 91 TYR cc_start: 0.7033 (m-80) cc_final: 0.6768 (m-80) REVERT: J 81 GLN cc_start: 0.6621 (mp10) cc_final: 0.6360 (tp-100) REVERT: K 81 GLN cc_start: 0.7626 (mp10) cc_final: 0.7144 (mm-40) REVERT: L 29 PHE cc_start: 0.7820 (t80) cc_final: 0.7576 (t80) REVERT: L 71 ILE cc_start: 0.9065 (tt) cc_final: 0.8779 (pt) REVERT: M 81 GLN cc_start: 0.7684 (mp10) cc_final: 0.6729 (tp40) REVERT: N 125 VAL cc_start: 0.9050 (t) cc_final: 0.8739 (p) REVERT: O 81 GLN cc_start: 0.7937 (mp10) cc_final: 0.7520 (mm110) REVERT: P 40 GLN cc_start: 0.9059 (tt0) cc_final: 0.8815 (tt0) REVERT: Q 81 GLN cc_start: 0.7690 (mp10) cc_final: 0.7408 (mm110) REVERT: Q 104 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8660 (mm-40) REVERT: R 91 TYR cc_start: 0.7868 (m-80) cc_final: 0.7660 (m-80) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2380 time to fit residues: 71.6178 Evaluate side-chains 104 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 0.0470 chunk 168 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 221 optimal weight: 0.0060 chunk 246 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN I 40 GLN K 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18795 Z= 0.130 Angle : 0.492 8.098 25704 Z= 0.264 Chirality : 0.042 0.149 3696 Planarity : 0.002 0.018 3108 Dihedral : 4.521 32.714 2772 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2709 helix: 2.48 (0.20), residues: 651 sheet: -2.07 (0.17), residues: 819 loop : -1.53 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.001 PHE A 29 TYR 0.014 0.003 TYR D 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.053 Fit side-chains REVERT: A 81 GLN cc_start: 0.7198 (mp10) cc_final: 0.6611 (mm-40) REVERT: A 121 GLN cc_start: 0.8348 (tt0) cc_final: 0.8094 (tt0) REVERT: C 81 GLN cc_start: 0.7543 (mp10) cc_final: 0.6849 (mm-40) REVERT: D 40 GLN cc_start: 0.8087 (tt0) cc_final: 0.7540 (tt0) REVERT: D 59 ASN cc_start: 0.8779 (t0) cc_final: 0.8403 (t0) REVERT: D 60 THR cc_start: 0.8386 (p) cc_final: 0.8148 (t) REVERT: E 40 GLN cc_start: 0.8356 (tt0) cc_final: 0.7742 (tt0) REVERT: E 59 ASN cc_start: 0.8767 (t0) cc_final: 0.8416 (t0) REVERT: E 81 GLN cc_start: 0.7327 (mp10) cc_final: 0.7074 (mp10) REVERT: G 81 GLN cc_start: 0.7675 (mp10) cc_final: 0.6561 (mm-40) REVERT: H 40 GLN cc_start: 0.8477 (tt0) cc_final: 0.8098 (tt0) REVERT: H 59 ASN cc_start: 0.8919 (t0) cc_final: 0.8625 (t0) REVERT: H 81 GLN cc_start: 0.6791 (mp10) cc_final: 0.6448 (mm-40) REVERT: I 81 GLN cc_start: 0.7267 (mp10) cc_final: 0.6674 (mm-40) REVERT: I 91 TYR cc_start: 0.7248 (m-80) cc_final: 0.7003 (m-80) REVERT: J 81 GLN cc_start: 0.6508 (mp10) cc_final: 0.6274 (tp-100) REVERT: J 91 TYR cc_start: 0.7946 (m-80) cc_final: 0.7642 (m-80) REVERT: K 29 PHE cc_start: 0.7453 (m-10) cc_final: 0.7238 (m-10) REVERT: K 81 GLN cc_start: 0.7659 (mp10) cc_final: 0.7086 (mm-40) REVERT: L 40 GLN cc_start: 0.8781 (tt0) cc_final: 0.8354 (tt0) REVERT: L 71 ILE cc_start: 0.9028 (tt) cc_final: 0.8687 (pt) REVERT: M 81 GLN cc_start: 0.7620 (mp10) cc_final: 0.6665 (tp40) REVERT: N 125 VAL cc_start: 0.8930 (t) cc_final: 0.8460 (p) REVERT: O 81 GLN cc_start: 0.8010 (mp10) cc_final: 0.7382 (mm110) REVERT: O 91 TYR cc_start: 0.6824 (m-80) cc_final: 0.6469 (m-80) REVERT: P 40 GLN cc_start: 0.8980 (tt0) cc_final: 0.8643 (tt0) REVERT: Q 81 GLN cc_start: 0.7639 (mp10) cc_final: 0.7367 (mm110) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2388 time to fit residues: 76.9774 Evaluate side-chains 114 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 249 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 71 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 40 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN E 121 GLN F 88 GLN G 40 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 40 GLN O 88 GLN ** R 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN U 40 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 18795 Z= 0.158 Angle : 0.488 7.242 25704 Z= 0.263 Chirality : 0.042 0.160 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.322 29.404 2772 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.05 % 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: -0.86 (0.17), residues: 2709 helix: 2.88 (0.21), residues: 651 sheet: -1.96 (0.17), residues: 819 loop : -1.45 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.002 PHE D 29 TYR 0.014 0.003 TYR D 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 2.046 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: A 81 GLN cc_start: 0.7308 (mp10) cc_final: 0.6732 (mm-40) REVERT: A 121 GLN cc_start: 0.8392 (tt0) cc_final: 0.8148 (tt0) REVERT: C 81 GLN cc_start: 0.7529 (mp10) cc_final: 0.6833 (mm-40) REVERT: D 35 GLN cc_start: 0.8549 (pp30) cc_final: 0.8174 (pp30) REVERT: D 38 VAL cc_start: 0.9162 (t) cc_final: 0.8939 (t) REVERT: D 40 GLN cc_start: 0.8094 (tt0) cc_final: 0.7548 (tt0) REVERT: D 59 ASN cc_start: 0.8851 (t0) cc_final: 0.8510 (t0) REVERT: E 38 VAL cc_start: 0.9405 (t) cc_final: 0.9139 (t) REVERT: E 40 GLN cc_start: 0.8413 (tt0) cc_final: 0.7756 (tt0) REVERT: E 59 ASN cc_start: 0.8846 (t0) cc_final: 0.8507 (t0) REVERT: E 81 GLN cc_start: 0.7349 (mp10) cc_final: 0.7073 (mp10) REVERT: G 81 GLN cc_start: 0.7682 (mp10) cc_final: 0.6893 (mp10) REVERT: H 40 GLN cc_start: 0.8494 (tt0) cc_final: 0.7940 (tt0) REVERT: H 59 ASN cc_start: 0.8897 (t0) cc_final: 0.8629 (t0) REVERT: H 81 GLN cc_start: 0.7048 (mp10) cc_final: 0.6793 (mm-40) REVERT: H 88 GLN cc_start: 0.7071 (mt0) cc_final: 0.6848 (mt0) REVERT: I 81 GLN cc_start: 0.7274 (mp10) cc_final: 0.6646 (mm-40) REVERT: I 91 TYR cc_start: 0.7182 (m-80) cc_final: 0.6941 (m-80) REVERT: K 81 GLN cc_start: 0.7617 (mp10) cc_final: 0.6984 (mm-40) REVERT: L 71 ILE cc_start: 0.8944 (tt) cc_final: 0.8588 (pt) REVERT: M 81 GLN cc_start: 0.7568 (mp10) cc_final: 0.6675 (tp40) REVERT: O 81 GLN cc_start: 0.8006 (mp10) cc_final: 0.7356 (mm110) REVERT: O 91 TYR cc_start: 0.6945 (m-80) cc_final: 0.6625 (m-80) REVERT: P 40 GLN cc_start: 0.9044 (tt0) cc_final: 0.8732 (tt0) REVERT: P 124 THR cc_start: 0.8473 (p) cc_final: 0.8262 (p) REVERT: Q 81 GLN cc_start: 0.7627 (mp10) cc_final: 0.7302 (mm110) outliers start: 2 outliers final: 1 residues processed: 159 average time/residue: 0.2372 time to fit residues: 63.6679 Evaluate side-chains 109 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 196 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 225 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN G 88 GLN H 35 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 40 GLN ** R 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18795 Z= 0.186 Angle : 0.497 9.915 25704 Z= 0.269 Chirality : 0.042 0.145 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.297 28.736 2772 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.05 % Allowed : 1.52 % Favored : 98.43 % 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: -0.74 (0.17), residues: 2709 helix: 2.96 (0.21), residues: 651 sheet: -1.80 (0.18), residues: 819 loop : -1.42 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE A 29 TYR 0.013 0.003 TYR D 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 2.055 Fit side-chains REVERT: A 81 GLN cc_start: 0.7309 (mp10) cc_final: 0.6725 (mm-40) REVERT: A 121 GLN cc_start: 0.8395 (tt0) cc_final: 0.8179 (tt0) REVERT: C 81 GLN cc_start: 0.7505 (mp10) cc_final: 0.6834 (mm-40) REVERT: D 35 GLN cc_start: 0.8498 (pp30) cc_final: 0.8056 (pp30) REVERT: D 59 ASN cc_start: 0.8849 (t0) cc_final: 0.8372 (t0) REVERT: E 40 GLN cc_start: 0.8567 (tt0) cc_final: 0.7890 (tt0) REVERT: E 81 GLN cc_start: 0.7387 (mp10) cc_final: 0.7067 (mp10) REVERT: G 81 GLN cc_start: 0.7651 (mp10) cc_final: 0.6801 (mp10) REVERT: H 40 GLN cc_start: 0.8556 (tt0) cc_final: 0.7897 (tt0) REVERT: H 59 ASN cc_start: 0.8910 (t0) cc_final: 0.8681 (t0) REVERT: H 81 GLN cc_start: 0.7112 (mp10) cc_final: 0.6800 (mm-40) REVERT: H 88 GLN cc_start: 0.7246 (mt0) cc_final: 0.6970 (mt0) REVERT: I 81 GLN cc_start: 0.7289 (mp10) cc_final: 0.6630 (mm-40) REVERT: I 114 THR cc_start: 0.9328 (m) cc_final: 0.9019 (p) REVERT: K 81 GLN cc_start: 0.7611 (mp10) cc_final: 0.7001 (mm-40) REVERT: K 91 TYR cc_start: 0.7515 (m-80) cc_final: 0.7291 (m-10) REVERT: L 71 ILE cc_start: 0.9011 (tt) cc_final: 0.8569 (pt) REVERT: M 81 GLN cc_start: 0.7591 (mp10) cc_final: 0.6676 (tp40) REVERT: O 81 GLN cc_start: 0.7994 (mp10) cc_final: 0.7388 (mm110) REVERT: O 91 TYR cc_start: 0.7007 (m-80) cc_final: 0.6767 (m-80) REVERT: P 40 GLN cc_start: 0.9097 (tt0) cc_final: 0.8595 (tt0) REVERT: Q 81 GLN cc_start: 0.7633 (mp10) cc_final: 0.7312 (mm110) REVERT: R 125 VAL cc_start: 0.9053 (t) cc_final: 0.8605 (p) outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.2422 time to fit residues: 64.5375 Evaluate side-chains 105 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 121 GLN E 121 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18795 Z= 0.350 Angle : 0.635 9.072 25704 Z= 0.338 Chirality : 0.045 0.193 3696 Planarity : 0.002 0.018 3108 Dihedral : 4.858 32.254 2772 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.87 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.75 (0.17), residues: 2709 helix: 2.84 (0.20), residues: 651 sheet: -1.62 (0.18), residues: 777 loop : -1.54 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.002 PHE H 29 TYR 0.026 0.004 TYR S 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.931 Fit side-chains REVERT: A 81 GLN cc_start: 0.7506 (mp10) cc_final: 0.6501 (tp40) REVERT: A 121 GLN cc_start: 0.8401 (tt0) cc_final: 0.8147 (tt0) REVERT: C 81 GLN cc_start: 0.7593 (mp10) cc_final: 0.6966 (mm-40) REVERT: D 35 GLN cc_start: 0.8707 (pp30) cc_final: 0.8211 (pp30) REVERT: E 40 GLN cc_start: 0.8489 (tt0) cc_final: 0.8202 (tt0) REVERT: E 81 GLN cc_start: 0.7498 (mp10) cc_final: 0.7118 (mp10) REVERT: G 81 GLN cc_start: 0.7678 (mp10) cc_final: 0.6776 (mp10) REVERT: H 40 GLN cc_start: 0.8616 (tt0) cc_final: 0.8103 (tt0) REVERT: H 81 GLN cc_start: 0.7306 (mp10) cc_final: 0.6980 (mm-40) REVERT: H 88 GLN cc_start: 0.7190 (mt0) cc_final: 0.6934 (mt0) REVERT: I 81 GLN cc_start: 0.7575 (mp10) cc_final: 0.6698 (mm-40) REVERT: I 114 THR cc_start: 0.9371 (m) cc_final: 0.9127 (p) REVERT: K 81 GLN cc_start: 0.7622 (mp10) cc_final: 0.7050 (mm-40) REVERT: L 29 PHE cc_start: 0.8052 (t80) cc_final: 0.7736 (t80) REVERT: L 71 ILE cc_start: 0.8990 (tt) cc_final: 0.8643 (pt) REVERT: M 81 GLN cc_start: 0.7700 (mp10) cc_final: 0.6728 (tp40) REVERT: O 81 GLN cc_start: 0.7960 (mp10) cc_final: 0.7088 (mm110) REVERT: O 91 TYR cc_start: 0.7153 (m-80) cc_final: 0.6909 (m-80) REVERT: P 40 GLN cc_start: 0.9157 (tt0) cc_final: 0.8698 (tt0) REVERT: Q 81 GLN cc_start: 0.7636 (mp10) cc_final: 0.7309 (mm110) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2443 time to fit residues: 55.2569 Evaluate side-chains 94 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN G 88 GLN H 88 GLN H 121 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18795 Z= 0.304 Angle : 0.603 9.964 25704 Z= 0.319 Chirality : 0.044 0.228 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.743 31.782 2772 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.87 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.32 (0.17), residues: 2709 helix: 1.82 (0.20), residues: 777 sheet: -2.21 (0.17), residues: 882 loop : -1.61 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE F 29 TYR 0.019 0.004 TYR B 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.980 Fit side-chains REVERT: A 81 GLN cc_start: 0.7457 (mp10) cc_final: 0.6498 (tp-100) REVERT: A 121 GLN cc_start: 0.8406 (tt0) cc_final: 0.8188 (tt0) REVERT: C 81 GLN cc_start: 0.7526 (mp10) cc_final: 0.6814 (mm-40) REVERT: D 35 GLN cc_start: 0.8621 (pp30) cc_final: 0.8130 (pp30) REVERT: E 40 GLN cc_start: 0.8603 (tt0) cc_final: 0.8323 (tt0) REVERT: E 81 GLN cc_start: 0.7413 (mp10) cc_final: 0.7109 (mp10) REVERT: G 81 GLN cc_start: 0.7644 (mp10) cc_final: 0.6756 (mp10) REVERT: H 40 GLN cc_start: 0.8628 (tt0) cc_final: 0.8110 (tt0) REVERT: H 59 ASN cc_start: 0.8993 (t0) cc_final: 0.8787 (t0) REVERT: H 81 GLN cc_start: 0.7318 (mp10) cc_final: 0.6964 (mm-40) REVERT: H 88 GLN cc_start: 0.7467 (mt0) cc_final: 0.7153 (mt0) REVERT: I 81 GLN cc_start: 0.7541 (mp10) cc_final: 0.6694 (mm-40) REVERT: I 114 THR cc_start: 0.9362 (m) cc_final: 0.9107 (p) REVERT: K 81 GLN cc_start: 0.7568 (mp10) cc_final: 0.7030 (mm-40) REVERT: L 71 ILE cc_start: 0.8917 (tt) cc_final: 0.8519 (pt) REVERT: M 81 GLN cc_start: 0.7559 (mp10) cc_final: 0.6649 (tp40) REVERT: O 81 GLN cc_start: 0.7763 (mp10) cc_final: 0.7098 (mm110) REVERT: O 91 TYR cc_start: 0.7173 (m-80) cc_final: 0.6876 (m-80) REVERT: P 40 GLN cc_start: 0.9096 (tt0) cc_final: 0.8584 (tt0) REVERT: Q 81 GLN cc_start: 0.7635 (mp10) cc_final: 0.7320 (mm110) REVERT: U 114 THR cc_start: 0.8839 (m) cc_final: 0.8473 (p) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2420 time to fit residues: 55.7697 Evaluate side-chains 101 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 179 optimal weight: 0.0370 chunk 130 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN C 88 GLN D 88 GLN D 121 GLN E 121 GLN F 88 GLN G 88 GLN K 40 GLN K 88 GLN L 40 GLN R 35 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18795 Z= 0.163 Angle : 0.499 10.596 25704 Z= 0.270 Chirality : 0.042 0.213 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.297 28.845 2772 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.05 % Allowed : 1.14 % Favored : 98.81 % 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: -0.77 (0.17), residues: 2709 helix: 2.90 (0.21), residues: 651 sheet: -1.71 (0.18), residues: 819 loop : -1.52 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.002 PHE H 29 TYR 0.017 0.003 TYR K 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.981 Fit side-chains REVERT: A 81 GLN cc_start: 0.7375 (mp10) cc_final: 0.6492 (tp-100) REVERT: C 8 LEU cc_start: 0.7648 (tt) cc_final: 0.6935 (tt) REVERT: C 59 ASN cc_start: 0.9008 (t0) cc_final: 0.8803 (t0) REVERT: C 81 GLN cc_start: 0.7535 (mp10) cc_final: 0.6814 (mm-40) REVERT: C 121 GLN cc_start: 0.8701 (tt0) cc_final: 0.8475 (tt0) REVERT: D 35 GLN cc_start: 0.8485 (pp30) cc_final: 0.7992 (pp30) REVERT: E 40 GLN cc_start: 0.8592 (tt0) cc_final: 0.8324 (tt0) REVERT: E 81 GLN cc_start: 0.7355 (mp10) cc_final: 0.7096 (mp10) REVERT: G 81 GLN cc_start: 0.7574 (mp10) cc_final: 0.6689 (mp10) REVERT: H 40 GLN cc_start: 0.8586 (tt0) cc_final: 0.7763 (tt0) REVERT: H 81 GLN cc_start: 0.7294 (mp10) cc_final: 0.6960 (mm-40) REVERT: H 88 GLN cc_start: 0.7163 (mt0) cc_final: 0.6764 (mt0) REVERT: I 81 GLN cc_start: 0.7489 (mp10) cc_final: 0.6637 (mm-40) REVERT: I 114 THR cc_start: 0.9315 (m) cc_final: 0.9033 (p) REVERT: K 81 GLN cc_start: 0.7522 (mp10) cc_final: 0.6943 (mm-40) REVERT: L 71 ILE cc_start: 0.8894 (tt) cc_final: 0.8491 (pt) REVERT: M 81 GLN cc_start: 0.7409 (mp10) cc_final: 0.6557 (tp40) REVERT: O 81 GLN cc_start: 0.7730 (mp10) cc_final: 0.7056 (mm110) REVERT: O 91 TYR cc_start: 0.6798 (m-80) cc_final: 0.6565 (m-80) REVERT: P 40 GLN cc_start: 0.9073 (tt0) cc_final: 0.8385 (tt0) REVERT: Q 81 GLN cc_start: 0.7596 (mp10) cc_final: 0.7289 (mm110) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.2377 time to fit residues: 59.1415 Evaluate side-chains 107 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 75 optimal weight: 0.0010 chunk 221 optimal weight: 0.9980 chunk 231 optimal weight: 0.1980 chunk 244 optimal weight: 0.5980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN C 88 GLN D 88 GLN F 88 GLN G 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18795 Z= 0.141 Angle : 0.473 9.253 25704 Z= 0.259 Chirality : 0.042 0.195 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.043 26.943 2772 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2709 helix: 3.03 (0.21), residues: 651 sheet: -1.54 (0.19), residues: 819 loop : -1.45 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.001 PHE E 29 TYR 0.015 0.003 TYR P 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 2.131 Fit side-chains REVERT: A 81 GLN cc_start: 0.7363 (mp10) cc_final: 0.6776 (mm-40) REVERT: C 59 ASN cc_start: 0.8993 (t0) cc_final: 0.8786 (t0) REVERT: C 81 GLN cc_start: 0.7509 (mp10) cc_final: 0.6739 (mm-40) REVERT: D 33 THR cc_start: 0.8976 (m) cc_final: 0.8317 (p) REVERT: D 35 GLN cc_start: 0.8413 (pp30) cc_final: 0.7923 (pp30) REVERT: E 40 GLN cc_start: 0.8553 (tt0) cc_final: 0.8313 (tt0) REVERT: E 81 GLN cc_start: 0.7364 (mp10) cc_final: 0.6496 (mm110) REVERT: G 81 GLN cc_start: 0.7579 (mp10) cc_final: 0.6726 (mp10) REVERT: H 40 GLN cc_start: 0.8505 (tt0) cc_final: 0.8016 (tt0) REVERT: H 81 GLN cc_start: 0.7295 (mp10) cc_final: 0.6923 (mm-40) REVERT: H 88 GLN cc_start: 0.7161 (mt0) cc_final: 0.6943 (mt0) REVERT: I 81 GLN cc_start: 0.7463 (mp10) cc_final: 0.6597 (mm-40) REVERT: K 81 GLN cc_start: 0.7473 (mp10) cc_final: 0.6957 (mm-40) REVERT: L 71 ILE cc_start: 0.8833 (tt) cc_final: 0.8375 (pt) REVERT: M 81 GLN cc_start: 0.7395 (mp10) cc_final: 0.6530 (tp40) REVERT: O 81 GLN cc_start: 0.7831 (mp10) cc_final: 0.7218 (mm110) REVERT: O 91 TYR cc_start: 0.6741 (m-80) cc_final: 0.6518 (m-80) REVERT: P 40 GLN cc_start: 0.9067 (tt0) cc_final: 0.8337 (tt0) REVERT: Q 81 GLN cc_start: 0.7584 (mp10) cc_final: 0.7256 (mm110) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.2431 time to fit residues: 60.5945 Evaluate side-chains 107 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 0.3980 chunk 271 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN D 121 GLN E 121 GLN F 88 GLN G 40 GLN G 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 35 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18795 Z= 0.205 Angle : 0.513 9.147 25704 Z= 0.279 Chirality : 0.043 0.181 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.176 28.102 2772 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.05 % Allowed : 0.24 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2709 helix: 3.02 (0.21), residues: 651 sheet: -1.52 (0.19), residues: 819 loop : -1.46 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.002 PHE E 29 TYR 0.015 0.003 TYR G 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.917 Fit side-chains REVERT: A 81 GLN cc_start: 0.7451 (mp10) cc_final: 0.6661 (tp-100) REVERT: C 81 GLN cc_start: 0.7463 (mp10) cc_final: 0.6686 (mm-40) REVERT: D 33 THR cc_start: 0.9027 (m) cc_final: 0.8391 (p) REVERT: D 35 GLN cc_start: 0.8488 (pp30) cc_final: 0.7891 (pp30) REVERT: E 40 GLN cc_start: 0.8547 (tt0) cc_final: 0.8212 (tt0) REVERT: E 81 GLN cc_start: 0.7390 (mp10) cc_final: 0.7137 (mp10) REVERT: G 81 GLN cc_start: 0.7585 (mp10) cc_final: 0.6719 (mp10) REVERT: H 40 GLN cc_start: 0.8531 (tt0) cc_final: 0.7985 (tt0) REVERT: H 81 GLN cc_start: 0.7477 (mp10) cc_final: 0.7010 (mm-40) REVERT: I 81 GLN cc_start: 0.7492 (mp10) cc_final: 0.6627 (mm-40) REVERT: K 81 GLN cc_start: 0.7511 (mp10) cc_final: 0.6938 (mm-40) REVERT: L 71 ILE cc_start: 0.8878 (tt) cc_final: 0.8472 (pt) REVERT: M 81 GLN cc_start: 0.7417 (mp10) cc_final: 0.6548 (tp40) REVERT: O 81 GLN cc_start: 0.7841 (mp10) cc_final: 0.7232 (mm110) REVERT: P 40 GLN cc_start: 0.9087 (tt0) cc_final: 0.8282 (tt0) REVERT: P 71 ILE cc_start: 0.9099 (tt) cc_final: 0.8743 (pt) REVERT: Q 81 GLN cc_start: 0.7595 (mp10) cc_final: 0.7272 (mm110) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2427 time to fit residues: 53.2753 Evaluate side-chains 104 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN F 88 GLN G 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.064475 restraints weight = 49181.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.066282 restraints weight = 29960.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.067546 restraints weight = 20472.018| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 18795 Z= 0.299 Angle : 0.589 8.336 25704 Z= 0.316 Chirality : 0.044 0.180 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.526 32.569 2772 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.06 (0.17), residues: 2709 helix: 1.91 (0.20), residues: 777 sheet: -1.73 (0.18), residues: 840 loop : -1.72 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE E 29 TYR 0.017 0.004 TYR R 91 =============================================================================== Job complete usr+sys time: 2911.38 seconds wall clock time: 55 minutes 1.52 seconds (3301.52 seconds total)