Starting phenix.real_space_refine (version: dev) on Sat May 14 11:16:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/05_2022/6nav_0397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/05_2022/6nav_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_0397/05_2022/6nav_0397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/05_2022/6nav_0397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/05_2022/6nav_0397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/05_2022/6nav_0397.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 10.07, per 1000 atoms: 0.54 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: 7.38 Conformation dependent library (CDL) restraints added in 3.0 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: 1.62 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: 6.96 Time building geometry restraints manager: 7.98 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 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. 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.800 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.170 Process input model: 51.360 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 % 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 *********************** 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 : 2.031 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2267 time to fit residues: 130.8192 Evaluate side-chains 114 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6415 ------------------------------------------------------------------------------- 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: 2.9990 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 J 81 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 18795 Z= 0.251 Angle : 0.561 8.360 25704 Z= 0.304 Chirality : 0.043 0.138 3696 Planarity : 0.002 0.013 3108 Dihedral : 5.296 40.473 2772 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % 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: -1.61 (0.16), residues: 2709 helix: 1.69 (0.20), residues: 651 sheet: -2.22 (0.17), residues: 819 loop : -1.71 (0.17), residues: 1239 *********************** 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 160 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.028 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2363 time to fit residues: 63.8262 Evaluate side-chains 81 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4938 ------------------------------------------------------------------------------- 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: 0.1980 chunk 76 optimal weight: 0.0060 chunk 206 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 0.1980 chunk 221 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 88 GLN I 40 GLN K 40 GLN M 88 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 18795 Z= 0.146 Angle : 0.487 8.121 25704 Z= 0.265 Chirality : 0.041 0.145 3696 Planarity : 0.002 0.018 3108 Dihedral : 4.557 33.263 2772 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.05 % 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: -1.11 (0.17), residues: 2709 helix: 2.58 (0.20), residues: 651 sheet: -2.10 (0.17), residues: 819 loop : -1.56 (0.18), residues: 1239 *********************** 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 165 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 2.012 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.2473 time to fit residues: 68.5591 Evaluate side-chains 88 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2148 time to fit residues: 3.0982 ------------------------------------------------------------------------------- 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: 0.7980 chunk 186 optimal weight: 0.0770 chunk 128 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 118 optimal weight: 0.0570 chunk 166 optimal weight: 0.2980 chunk 249 optimal weight: 0.9980 chunk 263 optimal weight: 0.0270 chunk 130 optimal weight: 0.0570 chunk 236 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN I 59 ASN K 40 GLN M 121 GLN ** R 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 121 GLN U 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 18795 Z= 0.109 Angle : 0.473 8.693 25704 Z= 0.253 Chirality : 0.041 0.161 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.148 28.114 2772 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.05 % 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: -0.90 (0.17), residues: 2709 helix: 2.74 (0.20), residues: 651 sheet: -1.89 (0.18), residues: 819 loop : -1.48 (0.18), residues: 1239 *********************** 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 162 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.180 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 162 average time/residue: 0.2366 time to fit residues: 64.7692 Evaluate side-chains 89 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1968 time to fit residues: 2.9098 ------------------------------------------------------------------------------- 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: 0.5980 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 225 optimal weight: 0.0670 chunk 182 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 121 GLN D 88 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 18795 Z= 0.178 Angle : 0.490 8.225 25704 Z= 0.267 Chirality : 0.042 0.162 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.168 28.018 2772 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.05 % 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: -0.69 (0.17), residues: 2709 helix: 2.98 (0.21), residues: 651 sheet: -1.72 (0.18), residues: 819 loop : -1.43 (0.18), residues: 1239 *********************** 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 142 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 2.039 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.2469 time to fit residues: 59.1582 Evaluate side-chains 85 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5490 ------------------------------------------------------------------------------- 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: 0.8980 chunk 237 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN D 88 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN G 88 GLN H 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 18795 Z= 0.271 Angle : 0.570 9.001 25704 Z= 0.306 Chirality : 0.043 0.176 3696 Planarity : 0.002 0.018 3108 Dihedral : 4.586 30.708 2772 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.56 (0.17), residues: 2709 helix: 2.96 (0.21), residues: 651 sheet: -1.44 (0.19), residues: 777 loop : -1.45 (0.17), residues: 1281 *********************** 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: 1 poor density : 133 time to evaluate : 1.928 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2485 time to fit residues: 56.5784 Evaluate side-chains 86 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.275 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2569 time to fit residues: 3.2987 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 0.0770 chunk 149 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 160 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN E 88 GLN F 88 GLN G 88 GLN H 35 GLN H 88 GLN K 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18795 Z= 0.208 Angle : 0.522 11.341 25704 Z= 0.282 Chirality : 0.043 0.233 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.400 29.173 2772 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.05 % 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: -0.83 (0.17), residues: 2709 helix: 2.87 (0.21), residues: 651 sheet: -1.98 (0.18), residues: 882 loop : -1.31 (0.19), residues: 1176 *********************** 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 128 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.2514 time to fit residues: 54.8928 Evaluate side-chains 86 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2422 time to fit residues: 3.1903 ------------------------------------------------------------------------------- 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: 3.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN D 88 GLN D 121 GLN E 88 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 18795 Z= 0.173 Angle : 0.496 7.678 25704 Z= 0.272 Chirality : 0.042 0.209 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.199 27.332 2772 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.17), residues: 2709 helix: 2.94 (0.21), residues: 651 sheet: -1.28 (0.19), residues: 777 loop : -1.63 (0.17), residues: 1281 *********************** 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 132 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2395 time to fit residues: 54.1232 Evaluate side-chains 87 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4364 ------------------------------------------------------------------------------- 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: 0.8980 chunk 252 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 221 optimal weight: 0.0470 chunk 231 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 88 GLN D 88 GLN E 88 GLN F 88 GLN G 40 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18795 Z= 0.170 Angle : 0.485 7.273 25704 Z= 0.267 Chirality : 0.042 0.211 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.131 27.086 2772 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.17), residues: 2709 helix: 2.99 (0.21), residues: 651 sheet: -1.20 (0.19), residues: 777 loop : -1.64 (0.17), residues: 1281 *********************** 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 119 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.052 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2412 time to fit residues: 48.9401 Evaluate side-chains 89 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7898 ------------------------------------------------------------------------------- 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: 0.0570 chunk 158 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 271 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 88 GLN D 59 ASN E 88 GLN E 121 GLN F 88 GLN G 88 GLN H 88 GLN H 121 GLN K 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 18795 Z= 0.163 Angle : 0.483 7.083 25704 Z= 0.267 Chirality : 0.042 0.207 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.041 26.373 2772 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 0.05 % 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: -0.47 (0.17), residues: 2709 helix: 3.07 (0.21), residues: 651 sheet: -1.12 (0.19), residues: 777 loop : -1.62 (0.17), residues: 1281 ********************** 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 115 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.133 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.2480 time to fit residues: 48.5806 Evaluate side-chains 90 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3937 ------------------------------------------------------------------------------- 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: 0.6980 chunk 230 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 199 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 216 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** E 88 GLN F 88 GLN G 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.066726 restraints weight = 48640.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068593 restraints weight = 29279.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069851 restraints weight = 19868.106| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18795 Z= 0.203 Angle : 0.513 9.326 25704 Z= 0.281 Chirality : 0.043 0.206 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.131 27.970 2772 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2709 helix: 3.07 (0.21), residues: 651 sheet: -1.15 (0.19), residues: 777 loop : -1.65 (0.17), residues: 1281 =============================================================================== Job complete usr+sys time: 2737.34 seconds wall clock time: 52 minutes 19.91 seconds (3139.91 seconds total)