Starting phenix.real_space_refine (version: dev) on Thu Mar 16 23:43:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2023/6dwb_8924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2023/6dwb_8924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2023/6dwb_8924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2023/6dwb_8924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2023/6dwb_8924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2023/6dwb_8924.pdb" } resolution = 3.3 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= 0.003 sd= 0.026 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 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-4893/modules/chem_data/mon_lib" Total number of atoms: 18360 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "H" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "I" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "J" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "P" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "S" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "U" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "V" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "W" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "X" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Y" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Z" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "a" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "b" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "c" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "d" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Time building chain proxies: 10.55, per 1000 atoms: 0.57 Number of scatterers: 18360 At special positions: 0 Unit cell: (93.15, 93.15, 202.5, 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 3720 8.00 N 3030 7.00 C 11610 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: 7.00 Conformation dependent library (CDL) restraints added in 2.7 seconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 78 removed outlier: 3.835A pdb=" N ASN G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 78 removed outlier: 3.835A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 78 removed outlier: 3.835A pdb=" N ASN J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN K 78 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.805A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN Q 78 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN S 78 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN T 78 " --> pdb=" O ALA T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE U 16 " --> pdb=" O VAL U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS U 37 " --> pdb=" O LYS U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN U 78 " --> pdb=" O ALA U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE V 16 " --> pdb=" O VAL V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS V 37 " --> pdb=" O LYS V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN V 78 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE W 16 " --> pdb=" O VAL W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR W 28 " --> pdb=" O GLN W 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS W 37 " --> pdb=" O LYS W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN W 78 " --> pdb=" O ALA W 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 20 removed outlier: 3.807A pdb=" N PHE X 16 " --> pdb=" O VAL X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 37 removed outlier: 3.672A pdb=" N THR X 28 " --> pdb=" O GLN X 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS X 37 " --> pdb=" O LYS X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN X 78 " --> pdb=" O ALA X 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 20 removed outlier: 3.805A pdb=" N PHE Y 16 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR Y 28 " --> pdb=" O GLN Y 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Y 37 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN Y 78 " --> pdb=" O ALA Y 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE Z 16 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR Z 28 " --> pdb=" O GLN Z 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Z 37 " --> pdb=" O LYS Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN Z 78 " --> pdb=" O ALA Z 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 20 removed outlier: 3.805A pdb=" N PHE a 16 " --> pdb=" O VAL a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR a 28 " --> pdb=" O GLN a 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS a 37 " --> pdb=" O LYS a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN a 78 " --> pdb=" O ALA a 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE b 16 " --> pdb=" O VAL b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 37 removed outlier: 3.670A pdb=" N THR b 28 " --> pdb=" O GLN b 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS b 37 " --> pdb=" O LYS b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE c 16 " --> pdb=" O VAL c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR c 28 " --> pdb=" O GLN c 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 78 removed outlier: 3.833A pdb=" N ASN c 78 " --> pdb=" O ALA c 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 20 removed outlier: 3.806A pdb=" N PHE d 16 " --> pdb=" O VAL d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 37 removed outlier: 3.671A pdb=" N THR d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS d 37 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 78 removed outlier: 3.834A pdb=" N ASN d 78 " --> pdb=" O ALA d 74 " (cutoff:3.500A) 1590 hydrogen bonds defined for protein. 4770 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: 5.31 Time building geometry restraints manager: 7.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 3270 1.29 - 1.35: 2790 1.35 - 1.42: 1830 1.42 - 1.48: 2760 1.48 - 1.54: 8040 Bond restraints: 18690 Sorted by residual: bond pdb=" CB TRP Y 5 " pdb=" CG TRP Y 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.08e+00 bond pdb=" CB TRP G 5 " pdb=" CG TRP G 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.07e+00 bond pdb=" CB TRP M 5 " pdb=" CG TRP M 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.07e+00 bond pdb=" CB TRP W 5 " pdb=" CG TRP W 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 bond pdb=" CB TRP a 5 " pdb=" CG TRP a 5 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.06e+00 ... (remaining 18685 not shown) Histogram of bond angle deviations from ideal: 102.61 - 108.86: 821 108.86 - 115.12: 10839 115.12 - 121.37: 10217 121.37 - 127.63: 3443 127.63 - 133.89: 120 Bond angle restraints: 25440 Sorted by residual: angle pdb=" N SER N 39 " pdb=" CA SER N 39 " pdb=" C SER N 39 " ideal model delta sigma weight residual 113.19 109.93 3.26 1.58e+00 4.01e-01 4.25e+00 angle pdb=" N SER M 39 " pdb=" CA SER M 39 " pdb=" C SER M 39 " ideal model delta sigma weight residual 113.19 109.93 3.26 1.58e+00 4.01e-01 4.25e+00 angle pdb=" N SER D 39 " pdb=" CA SER D 39 " pdb=" C SER D 39 " ideal model delta sigma weight residual 113.19 109.96 3.23 1.58e+00 4.01e-01 4.19e+00 angle pdb=" N SER E 39 " pdb=" CA SER E 39 " pdb=" C SER E 39 " ideal model delta sigma weight residual 113.19 109.96 3.23 1.58e+00 4.01e-01 4.18e+00 angle pdb=" N SER A 39 " pdb=" CA SER A 39 " pdb=" C SER A 39 " ideal model delta sigma weight residual 113.19 109.97 3.22 1.58e+00 4.01e-01 4.16e+00 ... (remaining 25435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.51: 9392 6.51 - 13.01: 1468 13.01 - 19.51: 360 19.51 - 26.02: 60 26.02 - 32.52: 60 Dihedral angle restraints: 11340 sinusoidal: 4350 harmonic: 6990 Sorted by residual: dihedral pdb=" CA ARG a 80 " pdb=" CB ARG a 80 " pdb=" CG ARG a 80 " pdb=" CD ARG a 80 " ideal model delta sinusoidal sigma weight residual -60.00 -92.52 32.52 3 1.50e+01 4.44e-03 5.37e+00 dihedral pdb=" CA ARG J 80 " pdb=" CB ARG J 80 " pdb=" CG ARG J 80 " pdb=" CD ARG J 80 " ideal model delta sinusoidal sigma weight residual -60.00 -92.50 32.50 3 1.50e+01 4.44e-03 5.36e+00 dihedral pdb=" CA ARG H 80 " pdb=" CB ARG H 80 " pdb=" CG ARG H 80 " pdb=" CD ARG H 80 " ideal model delta sinusoidal sigma weight residual -60.00 -92.48 32.48 3 1.50e+01 4.44e-03 5.35e+00 ... (remaining 11337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1346 0.022 - 0.044: 912 0.044 - 0.066: 441 0.066 - 0.089: 152 0.089 - 0.111: 59 Chirality restraints: 2910 Sorted by residual: chirality pdb=" CA PRO H 41 " pdb=" N PRO H 41 " pdb=" C PRO H 41 " pdb=" CB PRO H 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.06e-01 chirality pdb=" CA PRO I 41 " pdb=" N PRO I 41 " pdb=" C PRO I 41 " pdb=" CB PRO I 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.91e-01 chirality pdb=" CA PRO c 41 " pdb=" N PRO c 41 " pdb=" C PRO c 41 " pdb=" CB PRO c 41 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.81e-01 ... (remaining 2907 not shown) Planarity restraints: 3330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP N 40 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO N 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP a 40 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO a 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO a 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO a 41 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP U 40 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO U 41 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO U 41 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO U 41 " -0.017 5.00e-02 4.00e+02 ... (remaining 3327 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 533 2.71 - 3.26: 19243 3.26 - 3.80: 29140 3.80 - 4.35: 37006 4.35 - 4.90: 63240 Nonbonded interactions: 149162 Sorted by model distance: nonbonded pdb=" OD1 ASP H 10 " pdb=" OG SER N 49 " model vdw 2.161 2.440 nonbonded pdb=" OD1 ASP S 10 " pdb=" OG SER Y 49 " model vdw 2.217 2.440 nonbonded pdb=" OD1 ASP R 10 " pdb=" OG SER X 49 " model vdw 2.222 2.440 nonbonded pdb=" OD1 ASP A 10 " pdb=" OG SER G 49 " model vdw 2.228 2.440 nonbonded pdb=" OD1 ASP M 10 " pdb=" OG SER S 49 " model vdw 2.239 2.440 ... (remaining 149157 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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 11610 2.51 5 N 3030 2.21 5 O 3720 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.620 Check model and map are aligned: 0.290 Process input model: 47.080 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.007 0.032 18690 Z= 0.438 Angle : 0.655 3.431 25440 Z= 0.419 Chirality : 0.036 0.111 2910 Planarity : 0.005 0.031 3330 Dihedral : 7.211 32.525 6780 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -6.22 (0.07), residues: 2280 helix: -3.61 (0.05), residues: 1980 sheet: None (None), residues: 0 loop : -5.46 (0.22), residues: 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 2.094 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3051 time to fit residues: 210.9914 Evaluate side-chains 298 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 61 GLN C 61 GLN D 26 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN D 63 ASN E 61 GLN E 63 ASN F 61 GLN G 61 GLN H 61 GLN I 61 GLN J 61 GLN K 61 GLN L 61 GLN M 61 GLN N 61 GLN O 61 GLN P 61 GLN R 61 GLN S 61 GLN T 61 GLN V 61 GLN V 78 ASN W 61 GLN X 61 GLN Y 22 ASN Y 61 GLN Z 61 GLN a 61 GLN a 78 ASN c 61 GLN d 61 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 18690 Z= 0.183 Angle : 0.508 7.707 25440 Z= 0.289 Chirality : 0.033 0.099 2910 Planarity : 0.004 0.029 3330 Dihedral : 3.508 12.303 2520 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 1.16 % 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 (0.15), residues: 2280 helix: 1.20 (0.09), residues: 2040 sheet: None (None), residues: 0 loop : -4.85 (0.28), residues: 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 326 time to evaluate : 2.202 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 341 average time/residue: 0.2580 time to fit residues: 134.7012 Evaluate side-chains 279 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2017 time to fit residues: 6.3828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 0.0570 chunk 52 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: