Starting phenix.real_space_refine on Sun Mar 17 16:14:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2024/6dwb_8924.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2024/6dwb_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_2024/6dwb_8924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2024/6dwb_8924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2024/6dwb_8924.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dwb_8924/03_2024/6dwb_8924.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 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. 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-5265/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: 9.69, per 1000 atoms: 0.53 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: 7.17 Conformation dependent library (CDL) restraints added in 3.5 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: 1.41 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: 4.81 Time building geometry restraints manager: 7.76 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.840 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 46.590 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP I 5 PHE 0.013 0.002 PHE X 79 TYR 0.010 0.001 TYR E 57 ARG 0.003 0.001 ARG X 58 *********************** 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 : 2.058 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9080 (m-30) cc_final: 0.8798 (m-30) REVERT: B 15 LYS cc_start: 0.8215 (mttt) cc_final: 0.7963 (mtpp) REVERT: B 28 THR cc_start: 0.8594 (m) cc_final: 0.8330 (p) REVERT: B 77 GLN cc_start: 0.8108 (tt0) cc_final: 0.7855 (tp40) REVERT: C 28 THR cc_start: 0.8227 (m) cc_final: 0.7830 (p) REVERT: C 29 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7900 (mt-10) REVERT: C 37 LYS cc_start: 0.7550 (ttmt) cc_final: 0.6927 (tptt) REVERT: C 49 SER cc_start: 0.8374 (t) cc_final: 0.8046 (t) REVERT: C 57 TYR cc_start: 0.8222 (t80) cc_final: 0.7967 (t80) REVERT: D 11 ASP cc_start: 0.8395 (m-30) cc_final: 0.7988 (m-30) REVERT: D 37 LYS cc_start: 0.7488 (ttmt) cc_final: 0.6889 (tptt) REVERT: D 55 ASN cc_start: 0.8391 (t0) cc_final: 0.8131 (t0) REVERT: E 29 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8234 (mt-10) REVERT: E 37 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7096 (tptt) REVERT: F 6 SER cc_start: 0.8848 (m) cc_final: 0.8575 (p) REVERT: F 10 ASP cc_start: 0.8384 (m-30) cc_final: 0.7840 (m-30) REVERT: F 37 LYS cc_start: 0.8470 (ttmt) cc_final: 0.7272 (tptt) REVERT: G 6 SER cc_start: 0.8584 (m) cc_final: 0.8241 (p) REVERT: G 10 ASP cc_start: 0.8752 (m-30) cc_final: 0.8496 (m-30) REVERT: G 37 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7204 (tptt) REVERT: H 24 GLN cc_start: 0.8151 (mp10) cc_final: 0.7685 (mp10) REVERT: H 37 LYS cc_start: 0.8084 (ttmt) cc_final: 0.6749 (tptt) REVERT: I 23 LEU cc_start: 0.7209 (tp) cc_final: 0.6697 (tp) REVERT: I 24 GLN cc_start: 0.8064 (mp10) cc_final: 0.7610 (mp10) REVERT: I 27 VAL cc_start: 0.8296 (t) cc_final: 0.8094 (t) REVERT: I 28 THR cc_start: 0.8525 (m) cc_final: 0.8093 (m) REVERT: I 32 ASP cc_start: 0.8186 (m-30) cc_final: 0.7860 (m-30) REVERT: I 37 LYS cc_start: 0.7526 (ttmt) cc_final: 0.6172 (tptt) REVERT: I 57 TYR cc_start: 0.7642 (t80) cc_final: 0.7115 (t80) REVERT: K 10 ASP cc_start: 0.8071 (m-30) cc_final: 0.7469 (m-30) REVERT: K 32 ASP cc_start: 0.8415 (m-30) cc_final: 0.8082 (m-30) REVERT: K 37 LYS cc_start: 0.8214 (ttmt) cc_final: 0.6583 (tptt) REVERT: N 21 ASP cc_start: 0.7674 (m-30) cc_final: 0.7434 (m-30) REVERT: Q 33 LYS cc_start: 0.8244 (mttt) cc_final: 0.8034 (mtpp) REVERT: R 37 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8055 (ttmm) REVERT: R 49 SER cc_start: 0.8113 (t) cc_final: 0.7761 (p) REVERT: S 70 ASP cc_start: 0.7795 (m-30) cc_final: 0.7506 (m-30) REVERT: V 9 LEU cc_start: 0.4974 (mt) cc_final: 0.4648 (mt) REVERT: X 22 ASN cc_start: 0.7807 (p0) cc_final: 0.6937 (p0) REVERT: X 26 GLN cc_start: 0.7894 (mt0) cc_final: 0.6909 (mt0) REVERT: a 10 ASP cc_start: 0.6792 (m-30) cc_final: 0.6430 (m-30) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3059 time to fit residues: 211.2558 Evaluate side-chains 307 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.0870 chunk 190 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 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: 0.7301 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18690 Z= 0.167 Angle : 0.496 7.691 25440 Z= 0.285 Chirality : 0.033 0.098 2910 Planarity : 0.005 0.030 3330 Dihedral : 3.393 11.761 2520 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.11 % Allowed : 7.02 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 2280 helix: 1.07 (0.09), residues: 2040 sheet: None (None), residues: 0 loop : -4.83 (0.28), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 5 PHE 0.012 0.002 PHE d 16 TYR 0.016 0.001 TYR G 57 ARG 0.002 0.000 ARG W 80 *********************** 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 350 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 328 time to evaluate : 2.011 Fit side-chains revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8087 (m110) cc_final: 0.7614 (m110) REVERT: C 25 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8297 (p) REVERT: C 37 LYS cc_start: 0.7132 (ttmt) cc_final: 0.6443 (tptt) REVERT: C 66 LYS cc_start: 0.7979 (tptp) cc_final: 0.6526 (mttt) REVERT: D 11 ASP cc_start: 0.8089 (m-30) cc_final: 0.7491 (m-30) REVERT: D 22 ASN cc_start: 0.7810 (p0) cc_final: 0.7363 (p0) REVERT: D 32 ASP cc_start: 0.8004 (m-30) cc_final: 0.7741 (m-30) REVERT: D 77 GLN cc_start: 0.7889 (tt0) cc_final: 0.7661 (tp40) REVERT: E 37 LYS cc_start: 0.7509 (ttmt) cc_final: 0.6714 (tptt) REVERT: F 33 LYS cc_start: 0.8133 (mttm) cc_final: 0.7930 (mttt) REVERT: F 37 LYS cc_start: 0.8098 (ttmt) cc_final: 0.6960 (tptt) REVERT: F 53 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7111 (mm-30) REVERT: G 6 SER cc_start: 0.8927 (m) cc_final: 0.8637 (p) REVERT: G 10 ASP cc_start: 0.8658 (m-30) cc_final: 0.8373 (m-30) REVERT: G 32 ASP cc_start: 0.7671 (m-30) cc_final: 0.7359 (m-30) REVERT: G 37 LYS cc_start: 0.7796 (ttmt) cc_final: 0.6603 (tptt) REVERT: H 72 ASP cc_start: 0.8384 (m-30) cc_final: 0.8054 (m-30) REVERT: I 10 ASP cc_start: 0.8474 (m-30) cc_final: 0.8245 (m-30) REVERT: I 28 THR cc_start: 0.8649 (m) cc_final: 0.8164 (p) REVERT: K 10 ASP cc_start: 0.8296 (m-30) cc_final: 0.7831 (m-30) REVERT: K 32 ASP cc_start: 0.8095 (m-30) cc_final: 0.7880 (m-30) REVERT: K 37 LYS cc_start: 0.7731 (ttmt) cc_final: 0.7522 (ttpt) REVERT: L 33 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7631 (mtpp) REVERT: N 24 GLN cc_start: 0.7666 (mp10) cc_final: 0.7408 (mp10) REVERT: N 28 THR cc_start: 0.7990 (m) cc_final: 0.7478 (m) REVERT: N 72 ASP cc_start: 0.8149 (m-30) cc_final: 0.7932 (m-30) REVERT: P 32 ASP cc_start: 0.7313 (m-30) cc_final: 0.7082 (m-30) REVERT: Q 33 LYS cc_start: 0.8199 (mttt) cc_final: 0.7946 (mtmt) REVERT: T 70 ASP cc_start: 0.8051 (m-30) cc_final: 0.7803 (m-30) REVERT: U 10 ASP cc_start: 0.7314 (m-30) cc_final: 0.6772 (m-30) REVERT: W 32 ASP cc_start: 0.8103 (m-30) cc_final: 0.7794 (m-30) REVERT: W 57 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.8214 (t80) REVERT: W 76 ILE cc_start: 0.7629 (mt) cc_final: 0.7418 (mm) REVERT: X 24 GLN cc_start: 0.7473 (mp10) cc_final: 0.7013 (mp10) REVERT: a 10 ASP cc_start: 0.7450 (m-30) cc_final: 0.7172 (m-30) REVERT: b 69 LYS cc_start: 0.6642 (tttm) cc_final: 0.5184 (tptt) REVERT: c 32 ASP cc_start: 0.7610 (m-30) cc_final: 0.7391 (m-30) REVERT: c 70 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7573 (t0) REVERT: c 76 ILE cc_start: 0.7205 (mt) cc_final: 0.6732 (mm) REVERT: d 22 ASN cc_start: 0.6871 (p0) cc_final: 0.6424 (p0) REVERT: d 23 LEU cc_start: 0.7922 (tp) cc_final: 0.7502 (tp) REVERT: d 24 GLN cc_start: 0.7044 (mp10) cc_final: 0.6372 (mp10) outliers start: 22 outliers final: 11 residues processed: 341 average time/residue: 0.2885 time to fit residues: 149.1417 Evaluate side-chains 292 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 278 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain Q residue 49 SER Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain W residue 57 TYR Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain b residue 71 ILE Chi-restraints excluded: chain c residue 31 LEU Chi-restraints excluded: chain c residue 57 TYR Chi-restraints excluded: chain c residue 70 ASP 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: 0.8980 chunk 158 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN Q 61 GLN U 59 ASN W 61 GLN ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 GLN c 61 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18690 Z= 0.155 Angle : 0.431 6.013 25440 Z= 0.237 Chirality : 0.032 0.123 2910 Planarity : 0.003 0.022 3330 Dihedral : 3.235 18.424 2520 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.86 % Allowed : 10.35 % Favored : 88.79 % 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: 3.75 (0.17), residues: 2280 helix: 3.21 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -4.02 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 5 PHE 0.012 0.001 PHE T 68 TYR 0.017 0.001 TYR G 57 ARG 0.002 0.000 ARG W 58 *********************** REFINEMENT MACRO_CYCLE 3 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 354 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.7959 (tptp) cc_final: 0.6176 (mttm) REVERT: B 66 LYS cc_start: 0.7895 (tptp) cc_final: 0.6506 (ttmt) REVERT: C 27 VAL cc_start: 0.7874 (t) cc_final: 0.7546 (p) REVERT: C 37 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6466 (tmtt) REVERT: C 62 SER cc_start: 0.8226 (t) cc_final: 0.7909 (m) REVERT: C 66 LYS cc_start: 0.8154 (tptp) cc_final: 0.6630 (mttt) REVERT: D 11 ASP cc_start: 0.8016 (m-30) cc_final: 0.7540 (m-30) REVERT: D 32 ASP cc_start: 0.7987 (m-30) cc_final: 0.7730 (m-30) REVERT: D 37 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6526 (tmtt) REVERT: E 37 LYS cc_start: 0.7712 (ttmt) cc_final: 0.6956 (tptt) REVERT: E 66 LYS cc_start: 0.8201 (tptp) cc_final: 0.6387 (ttmt) REVERT: F 15 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7590 (ttmt) REVERT: F 37 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7104 (tptt) REVERT: G 6 SER cc_start: 0.9020 (m) cc_final: 0.8693 (p) REVERT: G 10 ASP cc_start: 0.8714 (m-30) cc_final: 0.8392 (m-30) REVERT: G 32 ASP cc_start: 0.7449 (m-30) cc_final: 0.7111 (m-30) REVERT: G 37 LYS cc_start: 0.8167 (ttmt) cc_final: 0.6927 (tptt) REVERT: J 28 THR cc_start: 0.8382 (m) cc_final: 0.7888 (m) REVERT: K 32 ASP cc_start: 0.8185 (m-30) cc_final: 0.7789 (m-30) REVERT: L 21 ASP cc_start: 0.8051 (m-30) cc_final: 0.7777 (m-30) REVERT: L 33 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7785 (mtpp) REVERT: M 53 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7751 (mm-30) REVERT: N 28 THR cc_start: 0.7974 (m) cc_final: 0.7666 (m) REVERT: P 32 ASP cc_start: 0.7233 (m-30) cc_final: 0.7033 (m-30) REVERT: Q 33 LYS cc_start: 0.8085 (mttt) cc_final: 0.7814 (mtpp) REVERT: T 32 ASP cc_start: 0.7232 (t0) cc_final: 0.6962 (m-30) REVERT: V 80 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5194 (pmt100) REVERT: W 28 THR cc_start: 0.7740 (m) cc_final: 0.6942 (m) REVERT: W 32 ASP cc_start: 0.8217 (m-30) cc_final: 0.7829 (m-30) REVERT: W 76 ILE cc_start: 0.7641 (mt) cc_final: 0.7361 (mm) REVERT: X 24 GLN cc_start: 0.7423 (mp10) cc_final: 0.7137 (mp10) REVERT: X 33 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7448 (mtmt) REVERT: X 63 ASN cc_start: 0.7784 (m-40) cc_final: 0.7551 (m-40) REVERT: Y 11 ASP cc_start: 0.7419 (m-30) cc_final: 0.7179 (m-30) REVERT: Y 59 ASN cc_start: 0.7399 (m-40) cc_final: 0.6927 (m110) REVERT: Z 32 ASP cc_start: 0.7745 (t0) cc_final: 0.7418 (m-30) REVERT: c 29 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7534 (mt-10) REVERT: d 23 LEU cc_start: 0.8105 (tp) cc_final: 0.7734 (tp) REVERT: d 24 GLN cc_start: 0.6890 (mp10) cc_final: 0.6528 (mp10) REVERT: d 71 ILE cc_start: 0.7976 (mt) cc_final: 0.7751 (mm) outliers start: 17 outliers final: 9 residues processed: 344 average time/residue: 0.2985 time to fit residues: 154.1929 Evaluate side-chains 294 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 284 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain I residue 15 LYS Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain c residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN E 61 GLN H 61 GLN I 61 GLN J 61 GLN L 61 GLN M 61 GLN R 61 GLN U 61 GLN a 61 GLN b 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18690 Z= 0.234 Angle : 0.498 6.069 25440 Z= 0.276 Chirality : 0.036 0.125 2910 Planarity : 0.003 0.021 3330 Dihedral : 3.602 18.586 2520 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.96 % Allowed : 11.26 % Favored : 87.78 % 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: 3.87 (0.17), residues: 2280 helix: 3.25 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.61 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 5 PHE 0.011 0.002 PHE N 79 TYR 0.027 0.002 TYR D 57 ARG 0.005 0.001 ARG M 58 *********************** REFINEMENT MACRO_CYCLE 4 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 350 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 331 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.7610 (t0) cc_final: 0.7089 (t0) REVERT: B 66 LYS cc_start: 0.8140 (tptp) cc_final: 0.6113 (mttt) REVERT: C 25 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8141 (p) REVERT: C 66 LYS cc_start: 0.8551 (tptp) cc_final: 0.6687 (mttt) REVERT: D 32 ASP cc_start: 0.8039 (m-30) cc_final: 0.7805 (m-30) REVERT: D 37 LYS cc_start: 0.7517 (ttmt) cc_final: 0.6699 (tmtt) REVERT: E 37 LYS cc_start: 0.7766 (ttmt) cc_final: 0.6852 (tptt) REVERT: E 66 LYS cc_start: 0.8164 (tptp) cc_final: 0.6320 (ttmt) REVERT: F 37 LYS cc_start: 0.8153 (ttmt) cc_final: 0.6953 (tptt) REVERT: G 10 ASP cc_start: 0.8679 (m-30) cc_final: 0.8309 (m-30) REVERT: G 32 ASP cc_start: 0.7756 (m-30) cc_final: 0.7498 (m-30) REVERT: I 72 ASP cc_start: 0.8290 (m-30) cc_final: 0.7994 (m-30) REVERT: J 28 THR cc_start: 0.8457 (m) cc_final: 0.8230 (m) REVERT: J 80 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.5593 (pmt100) REVERT: K 32 ASP cc_start: 0.7969 (m-30) cc_final: 0.7577 (m-30) REVERT: K 66 LYS cc_start: 0.8065 (tptp) cc_final: 0.7844 (tptm) REVERT: K 80 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.5194 (pmt100) REVERT: L 21 ASP cc_start: 0.8211 (m-30) cc_final: 0.7870 (m-30) REVERT: N 28 THR cc_start: 0.8141 (m) cc_final: 0.7287 (p) REVERT: N 32 ASP cc_start: 0.7852 (m-30) cc_final: 0.7438 (m-30) REVERT: O 33 LYS cc_start: 0.7933 (mttm) cc_final: 0.7700 (mtmm) REVERT: P 80 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.5901 (pmt100) REVERT: Q 66 LYS cc_start: 0.7704 (tptp) cc_final: 0.7266 (tptt) REVERT: T 6 SER cc_start: 0.8650 (m) cc_final: 0.8265 (p) REVERT: T 32 ASP cc_start: 0.6984 (t0) cc_final: 0.6700 (m-30) REVERT: T 53 GLU cc_start: 0.8018 (tp30) cc_final: 0.7733 (tp30) REVERT: T 77 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8411 (tp-100) REVERT: U 80 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.5314 (pmt100) REVERT: V 33 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7378 (mttp) REVERT: W 32 ASP cc_start: 0.8323 (m-30) cc_final: 0.7855 (m-30) REVERT: X 6 SER cc_start: 0.9032 (m) cc_final: 0.8776 (p) REVERT: X 33 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7452 (mtmt) REVERT: Y 6 SER cc_start: 0.8306 (m) cc_final: 0.7786 (p) REVERT: Y 33 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7062 (mttt) REVERT: Z 17 ASP cc_start: 0.7944 (m-30) cc_final: 0.7728 (m-30) REVERT: Z 53 GLU cc_start: 0.7082 (tp30) cc_final: 0.6816 (mm-30) REVERT: Z 66 LYS cc_start: 0.8017 (tptp) cc_final: 0.7674 (tptm) REVERT: a 69 LYS cc_start: 0.7927 (tttm) cc_final: 0.6730 (ttmt) REVERT: b 33 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7369 (mttp) REVERT: c 49 SER cc_start: 0.7772 (m) cc_final: 0.7527 (p) REVERT: c 53 GLU cc_start: 0.7650 (tp30) cc_final: 0.7077 (mm-30) REVERT: c 75 ILE cc_start: 0.7404 (mm) cc_final: 0.7087 (mt) REVERT: c 76 ILE cc_start: 0.7399 (mt) cc_final: 0.7002 (mm) REVERT: c 77 GLN cc_start: 0.8524 (tp40) cc_final: 0.8128 (tp40) REVERT: d 29 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7441 (mt-10) outliers start: 19 outliers final: 7 residues processed: 343 average time/residue: 0.3200 time to fit residues: 162.8653 Evaluate side-chains 304 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 291 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain P residue 80 ARG Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 33 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 182 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN I 61 GLN J 61 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 GLN U 61 GLN V 59 ASN a 59 ASN c 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18690 Z= 0.248 Angle : 0.463 7.965 25440 Z= 0.254 Chirality : 0.035 0.111 2910 Planarity : 0.003 0.023 3330 Dihedral : 3.460 27.793 2520 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.96 % Allowed : 11.82 % Favored : 87.22 % 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: 4.17 (0.17), residues: 2280 helix: 3.45 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.53 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 5 PHE 0.008 0.001 PHE U 16 TYR 0.017 0.002 TYR G 57 ARG 0.004 0.001 ARG V 80 *********************** REFINEMENT MACRO_CYCLE 5 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 326 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 307 time to evaluate : 2.075 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.8396 (t0) cc_final: 0.7999 (t0) REVERT: B 66 LYS cc_start: 0.8140 (tptp) cc_final: 0.6130 (mttt) REVERT: C 27 VAL cc_start: 0.8280 (t) cc_final: 0.8013 (p) REVERT: C 66 LYS cc_start: 0.8654 (tptp) cc_final: 0.6670 (mttt) REVERT: D 32 ASP cc_start: 0.7839 (m-30) cc_final: 0.7629 (m-30) REVERT: D 37 LYS cc_start: 0.7509 (ttmt) cc_final: 0.6677 (tmtt) REVERT: E 37 LYS cc_start: 0.7793 (ttmt) cc_final: 0.6854 (tptt) REVERT: E 66 LYS cc_start: 0.8158 (tptp) cc_final: 0.6298 (ttmt) REVERT: F 37 LYS cc_start: 0.8116 (ttmt) cc_final: 0.6943 (tptt) REVERT: G 32 ASP cc_start: 0.7435 (m-30) cc_final: 0.7190 (m-30) REVERT: I 72 ASP cc_start: 0.8115 (m-30) cc_final: 0.7901 (m-30) REVERT: J 28 THR cc_start: 0.8335 (m) cc_final: 0.8109 (m) REVERT: K 32 ASP cc_start: 0.7856 (m-30) cc_final: 0.7509 (m-30) REVERT: L 21 ASP cc_start: 0.8201 (m-30) cc_final: 0.8000 (m-30) REVERT: L 53 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8569 (mm-30) REVERT: N 28 THR cc_start: 0.8126 (m) cc_final: 0.7258 (p) REVERT: N 32 ASP cc_start: 0.7826 (m-30) cc_final: 0.7415 (m-30) REVERT: O 33 LYS cc_start: 0.7940 (mttm) cc_final: 0.7705 (mtmm) REVERT: O 80 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.5866 (pmt100) REVERT: P 80 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.5542 (pmt100) REVERT: Q 53 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8511 (mm-30) REVERT: Q 80 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.5038 (pmt100) REVERT: T 6 SER cc_start: 0.8663 (m) cc_final: 0.8325 (p) REVERT: T 32 ASP cc_start: 0.6917 (t0) cc_final: 0.6629 (m-30) REVERT: T 53 GLU cc_start: 0.8288 (tp30) cc_final: 0.7977 (mm-30) REVERT: V 33 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7436 (mttt) REVERT: V 66 LYS cc_start: 0.7813 (tptp) cc_final: 0.7560 (tptp) REVERT: W 32 ASP cc_start: 0.8251 (m-30) cc_final: 0.7672 (m-30) REVERT: X 6 SER cc_start: 0.9093 (m) cc_final: 0.8886 (p) REVERT: X 33 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7458 (mtmt) REVERT: Y 6 SER cc_start: 0.8299 (m) cc_final: 0.7850 (p) REVERT: Y 33 LYS cc_start: 0.7631 (mptt) cc_final: 0.7084 (mttt) REVERT: Z 32 ASP cc_start: 0.8089 (m-30) cc_final: 0.7757 (m-30) REVERT: Z 66 LYS cc_start: 0.8091 (tptp) cc_final: 0.7810 (tptm) REVERT: a 78 ASN cc_start: 0.7251 (p0) cc_final: 0.7001 (p0) REVERT: b 33 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7447 (mttm) REVERT: c 53 GLU cc_start: 0.7599 (tp30) cc_final: 0.6933 (mm-30) REVERT: c 77 GLN cc_start: 0.8450 (tp40) cc_final: 0.8077 (tp40) REVERT: d 29 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7529 (mt-10) outliers start: 19 outliers final: 12 residues processed: 319 average time/residue: 0.2956 time to fit residues: 141.9091 Evaluate side-chains 309 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 294 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 80 ARG Chi-restraints excluded: chain Q residue 80 ARG Chi-restraints excluded: chain R residue 6 SER Chi-restraints excluded: chain V residue 6 SER Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain a residue 79 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN I 61 GLN J 61 GLN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN O 24 GLN S 61 GLN U 59 ASN V 59 ASN d 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 18690 Z= 0.363 Angle : 0.534 7.253 25440 Z= 0.292 Chirality : 0.039 0.124 2910 Planarity : 0.003 0.026 3330 Dihedral : 3.823 36.843 2520 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.62 % Allowed : 11.82 % Favored : 86.57 % 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: 3.89 (0.17), residues: 2280 helix: 3.23 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.36 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 5 PHE 0.011 0.002 PHE U 16 TYR 0.023 0.003 TYR D 57 ARG 0.004 0.001 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 6 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 340 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 308 time to evaluate : 2.168 Fit side-chains REVERT: B 55 ASN cc_start: 0.8496 (t0) cc_final: 0.8007 (t0) REVERT: B 66 LYS cc_start: 0.8240 (tptp) cc_final: 0.6279 (mttt) REVERT: C 66 LYS cc_start: 0.8648 (tptp) cc_final: 0.6645 (mttt) REVERT: D 37 LYS cc_start: 0.7870 (ttmt) cc_final: 0.6950 (tmtt) REVERT: D 66 LYS cc_start: 0.8273 (tptp) cc_final: 0.6258 (mttm) REVERT: E 37 LYS cc_start: 0.7861 (ttmt) cc_final: 0.6928 (tptt) REVERT: E 53 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7672 (mm-30) REVERT: E 66 LYS cc_start: 0.8124 (tptp) cc_final: 0.6365 (ttmt) REVERT: F 37 LYS cc_start: 0.7735 (ttmt) cc_final: 0.6584 (tptt) REVERT: F 80 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7475 (ptt90) REVERT: G 32 ASP cc_start: 0.7763 (m-30) cc_final: 0.7499 (m-30) REVERT: I 72 ASP cc_start: 0.8352 (m-30) cc_final: 0.8083 (m-30) REVERT: I 80 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6070 (ptt90) REVERT: J 80 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.5619 (pmt100) REVERT: K 32 ASP cc_start: 0.7852 (m-30) cc_final: 0.7510 (m-30) REVERT: K 80 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.5338 (pmt100) REVERT: L 21 ASP cc_start: 0.8142 (m-30) cc_final: 0.7922 (m-30) REVERT: L 57 TYR cc_start: 0.9054 (t80) cc_final: 0.8718 (t80) REVERT: L 80 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6769 (pmt100) REVERT: M 53 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8589 (mm-30) REVERT: N 28 THR cc_start: 0.8117 (m) cc_final: 0.7170 (p) REVERT: N 32 ASP cc_start: 0.7852 (m-30) cc_final: 0.7439 (m-30) REVERT: N 80 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6108 (pmt100) REVERT: O 32 ASP cc_start: 0.7928 (m-30) cc_final: 0.7558 (m-30) REVERT: O 33 LYS cc_start: 0.7771 (mttm) cc_final: 0.7545 (mtmm) REVERT: O 53 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8247 (mm-30) REVERT: O 80 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.5767 (pmt100) REVERT: T 6 SER cc_start: 0.8639 (m) cc_final: 0.8348 (p) REVERT: T 32 ASP cc_start: 0.7020 (t0) cc_final: 0.6473 (m-30) REVERT: T 53 GLU cc_start: 0.8405 (tp30) cc_final: 0.8054 (mm-30) REVERT: U 53 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7618 (mm-30) REVERT: U 80 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.5350 (pmt100) REVERT: V 33 LYS cc_start: 0.7812 (mtmm) cc_final: 0.7452 (mttt) REVERT: W 10 ASP cc_start: 0.8248 (m-30) cc_final: 0.7823 (m-30) REVERT: W 32 ASP cc_start: 0.8278 (m-30) cc_final: 0.7828 (m-30) REVERT: X 6 SER cc_start: 0.9093 (m) cc_final: 0.8887 (p) REVERT: X 33 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7561 (mtmt) REVERT: Y 6 SER cc_start: 0.8275 (m) cc_final: 0.7877 (p) REVERT: Y 33 LYS cc_start: 0.7602 (mptt) cc_final: 0.7111 (mttt) REVERT: Y 80 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7231 (ptt90) REVERT: Z 53 GLU cc_start: 0.7671 (tp30) cc_final: 0.7435 (mm-30) REVERT: a 10 ASP cc_start: 0.7652 (m-30) cc_final: 0.7388 (m-30) REVERT: b 33 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7444 (mttp) REVERT: c 53 GLU cc_start: 0.7627 (tp30) cc_final: 0.6974 (mm-30) outliers start: 32 outliers final: 20 residues processed: 334 average time/residue: 0.3230 time to fit residues: 158.5992 Evaluate side-chains 323 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 294 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain I residue 80 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain R residue 6 SER Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 6 SER Chi-restraints excluded: chain Y residue 18 THR Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain d residue 49 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN I 61 GLN J 61 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN S 61 GLN U 59 ASN U 61 GLN V 59 ASN Y 59 ASN Z 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18690 Z= 0.158 Angle : 0.416 8.913 25440 Z= 0.228 Chirality : 0.032 0.106 2910 Planarity : 0.003 0.025 3330 Dihedral : 3.331 27.068 2520 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.81 % Allowed : 12.42 % Favored : 86.77 % 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: 4.46 (0.17), residues: 2280 helix: 3.65 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.42 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 5 PHE 0.007 0.001 PHE O 79 TYR 0.015 0.001 TYR G 57 ARG 0.005 0.000 ARG Q 80 *********************** REFINEMENT MACRO_CYCLE 7 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 320 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 304 time to evaluate : 2.065 Fit side-chains REVERT: B 55 ASN cc_start: 0.8366 (t0) cc_final: 0.7992 (t0) REVERT: B 66 LYS cc_start: 0.8135 (tptp) cc_final: 0.6095 (mttt) REVERT: C 66 LYS cc_start: 0.8628 (tptp) cc_final: 0.6655 (mttt) REVERT: D 37 LYS cc_start: 0.7570 (ttmt) cc_final: 0.6627 (tmtt) REVERT: D 66 LYS cc_start: 0.8188 (tptp) cc_final: 0.6180 (mttm) REVERT: E 37 LYS cc_start: 0.7789 (ttmt) cc_final: 0.6875 (tptt) REVERT: E 66 LYS cc_start: 0.8032 (tptp) cc_final: 0.6260 (ttmt) REVERT: F 37 LYS cc_start: 0.7687 (ttmt) cc_final: 0.6543 (tptt) REVERT: G 32 ASP cc_start: 0.7744 (m-30) cc_final: 0.7532 (m-30) REVERT: I 32 ASP cc_start: 0.7630 (m-30) cc_final: 0.7122 (m-30) REVERT: K 32 ASP cc_start: 0.7556 (m-30) cc_final: 0.7217 (m-30) REVERT: L 21 ASP cc_start: 0.8205 (m-30) cc_final: 0.7989 (m-30) REVERT: L 53 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8494 (mm-30) REVERT: L 80 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6344 (pmt100) REVERT: M 53 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8448 (mm-30) REVERT: N 28 THR cc_start: 0.8099 (m) cc_final: 0.7267 (p) REVERT: N 32 ASP cc_start: 0.7766 (m-30) cc_final: 0.7370 (m-30) REVERT: N 57 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8081 (t80) REVERT: O 33 LYS cc_start: 0.7690 (mttm) cc_final: 0.7428 (mtmm) REVERT: Q 53 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8472 (mm-30) REVERT: R 77 GLN cc_start: 0.8372 (tp40) cc_final: 0.8115 (tp40) REVERT: S 53 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8397 (mm-30) REVERT: T 32 ASP cc_start: 0.6972 (t0) cc_final: 0.6435 (m-30) REVERT: T 53 GLU cc_start: 0.8305 (tp30) cc_final: 0.8043 (mm-30) REVERT: U 32 ASP cc_start: 0.7412 (m-30) cc_final: 0.7142 (m-30) REVERT: V 33 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7332 (mttp) REVERT: W 29 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7647 (mt-10) REVERT: W 32 ASP cc_start: 0.8149 (m-30) cc_final: 0.7922 (m-30) REVERT: W 69 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7680 (tmtt) REVERT: X 33 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7486 (mtmt) REVERT: Y 6 SER cc_start: 0.8265 (m) cc_final: 0.7942 (p) REVERT: Y 33 LYS cc_start: 0.7563 (mptt) cc_final: 0.7070 (mttt) REVERT: a 10 ASP cc_start: 0.7726 (m-30) cc_final: 0.7464 (m-30) REVERT: a 11 ASP cc_start: 0.8224 (m-30) cc_final: 0.7924 (m-30) REVERT: b 33 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7420 (mttm) REVERT: c 53 GLU cc_start: 0.7596 (tp30) cc_final: 0.6935 (mm-30) REVERT: d 11 ASP cc_start: 0.8370 (m-30) cc_final: 0.8145 (m-30) outliers start: 16 outliers final: 9 residues processed: 315 average time/residue: 0.2861 time to fit residues: 137.1913 Evaluate side-chains 301 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 290 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain c residue 76 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 137 optimal weight: 0.1980 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN I 61 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN d 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18690 Z= 0.217 Angle : 0.441 8.242 25440 Z= 0.241 Chirality : 0.034 0.109 2910 Planarity : 0.003 0.030 3330 Dihedral : 3.473 28.070 2520 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.31 % Allowed : 12.27 % Favored : 86.41 % 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: 4.41 (0.17), residues: 2280 helix: 3.62 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.48 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 5 PHE 0.008 0.001 PHE H 16 TYR 0.016 0.002 TYR G 57 ARG 0.008 0.000 ARG M 80 *********************** REFINEMENT MACRO_CYCLE 8 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 324 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 2.126 Fit side-chains REVERT: A 80 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7054 (ptt90) REVERT: B 55 ASN cc_start: 0.8408 (t0) cc_final: 0.8011 (t0) REVERT: B 66 LYS cc_start: 0.8155 (tptp) cc_final: 0.6094 (mttt) REVERT: C 66 LYS cc_start: 0.8666 (tptp) cc_final: 0.6654 (mttt) REVERT: D 37 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7096 (tmtt) REVERT: D 66 LYS cc_start: 0.8214 (tptp) cc_final: 0.6240 (mttm) REVERT: E 37 LYS cc_start: 0.7807 (ttmt) cc_final: 0.6884 (tptt) REVERT: E 66 LYS cc_start: 0.8075 (tptp) cc_final: 0.6222 (ttmt) REVERT: F 37 LYS cc_start: 0.7709 (ttmt) cc_final: 0.6566 (tptt) REVERT: G 32 ASP cc_start: 0.7763 (m-30) cc_final: 0.7559 (m-30) REVERT: G 80 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6992 (ptt90) REVERT: H 80 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.5922 (pmt100) REVERT: I 32 ASP cc_start: 0.7669 (m-30) cc_final: 0.7146 (m-30) REVERT: J 80 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.5606 (pmt100) REVERT: K 32 ASP cc_start: 0.7596 (m-30) cc_final: 0.7257 (m-30) REVERT: K 80 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.5674 (ptt90) REVERT: L 21 ASP cc_start: 0.8153 (m-30) cc_final: 0.7942 (m-30) REVERT: L 53 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8393 (mm-30) REVERT: L 80 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6257 (pmt100) REVERT: M 53 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8429 (mm-30) REVERT: N 28 THR cc_start: 0.8117 (m) cc_final: 0.7254 (p) REVERT: N 32 ASP cc_start: 0.7782 (m-30) cc_final: 0.7396 (m-30) REVERT: N 57 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7956 (t80) REVERT: O 32 ASP cc_start: 0.7861 (m-30) cc_final: 0.7505 (m-30) REVERT: O 33 LYS cc_start: 0.7741 (mttm) cc_final: 0.7482 (mtmm) REVERT: O 80 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.5832 (pmt100) REVERT: P 53 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8541 (mm-30) REVERT: Q 53 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8308 (mm-30) REVERT: R 77 GLN cc_start: 0.8406 (tp40) cc_final: 0.8119 (tp40) REVERT: S 53 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8326 (mm-30) REVERT: T 32 ASP cc_start: 0.6977 (t0) cc_final: 0.6450 (m-30) REVERT: T 53 GLU cc_start: 0.8386 (tp30) cc_final: 0.8133 (mm-30) REVERT: U 32 ASP cc_start: 0.7417 (m-30) cc_final: 0.7129 (m-30) REVERT: V 33 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7348 (mttp) REVERT: W 32 ASP cc_start: 0.8161 (m-30) cc_final: 0.7937 (m-30) REVERT: W 69 LYS cc_start: 0.7918 (tmtt) cc_final: 0.7715 (tmtt) REVERT: X 33 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7562 (mtmt) REVERT: Y 6 SER cc_start: 0.8216 (m) cc_final: 0.7920 (p) REVERT: Y 33 LYS cc_start: 0.7575 (mptt) cc_final: 0.7098 (mttt) REVERT: Y 80 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.4032 (ttm170) REVERT: Z 32 ASP cc_start: 0.8247 (m-30) cc_final: 0.7833 (m-30) REVERT: a 10 ASP cc_start: 0.7652 (m-30) cc_final: 0.7395 (m-30) REVERT: a 11 ASP cc_start: 0.8288 (m-30) cc_final: 0.7959 (m-30) REVERT: b 33 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7423 (mttm) REVERT: c 53 GLU cc_start: 0.7578 (tp30) cc_final: 0.6910 (mm-30) REVERT: d 11 ASP cc_start: 0.8364 (m-30) cc_final: 0.8132 (m-30) outliers start: 26 outliers final: 13 residues processed: 317 average time/residue: 0.3019 time to fit residues: 142.6907 Evaluate side-chains 317 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 80 ARG Chi-restraints excluded: chain K residue 33 LYS Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain a residue 39 SER Chi-restraints excluded: chain d residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18690 Z= 0.145 Angle : 0.398 8.199 25440 Z= 0.217 Chirality : 0.032 0.103 2910 Planarity : 0.003 0.025 3330 Dihedral : 3.331 25.422 2520 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.16 % Allowed : 12.32 % Favored : 86.52 % 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: 4.70 (0.17), residues: 2280 helix: 3.82 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.48 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP N 5 PHE 0.006 0.001 PHE K 16 TYR 0.014 0.001 TYR G 57 ARG 0.007 0.000 ARG M 80 *********************** REFINEMENT MACRO_CYCLE 9 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 333 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 310 time to evaluate : 2.196 Fit side-chains REVERT: A 80 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7210 (ptt90) REVERT: B 55 ASN cc_start: 0.7553 (t0) cc_final: 0.7164 (t0) REVERT: B 66 LYS cc_start: 0.8175 (tptp) cc_final: 0.6551 (ttmt) REVERT: C 66 LYS cc_start: 0.8662 (tptp) cc_final: 0.6728 (mttt) REVERT: D 3 THR cc_start: 0.7956 (m) cc_final: 0.7747 (t) REVERT: D 37 LYS cc_start: 0.7565 (ttmt) cc_final: 0.6632 (tmtt) REVERT: D 66 LYS cc_start: 0.8061 (tptp) cc_final: 0.6102 (mttm) REVERT: E 37 LYS cc_start: 0.7778 (ttmt) cc_final: 0.6815 (tptt) REVERT: E 66 LYS cc_start: 0.8039 (tptp) cc_final: 0.6196 (ttmt) REVERT: F 37 LYS cc_start: 0.7725 (ttmt) cc_final: 0.6640 (tptt) REVERT: G 32 ASP cc_start: 0.7883 (m-30) cc_final: 0.7578 (m-30) REVERT: H 80 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.5875 (pmt100) REVERT: I 32 ASP cc_start: 0.7589 (m-30) cc_final: 0.7046 (m-30) REVERT: J 28 THR cc_start: 0.8269 (m) cc_final: 0.8020 (m) REVERT: K 32 ASP cc_start: 0.7529 (m-30) cc_final: 0.7200 (m-30) REVERT: K 80 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.5614 (ptt90) REVERT: L 21 ASP cc_start: 0.8123 (m-30) cc_final: 0.7902 (m-30) REVERT: L 53 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8305 (mm-30) REVERT: L 80 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6219 (pmt100) REVERT: M 53 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8369 (mm-30) REVERT: N 28 THR cc_start: 0.8096 (m) cc_final: 0.7265 (p) REVERT: N 32 ASP cc_start: 0.7722 (m-30) cc_final: 0.7318 (m-30) REVERT: N 57 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.8201 (t80) REVERT: O 33 LYS cc_start: 0.7874 (mttm) cc_final: 0.7601 (mtmm) REVERT: P 53 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8672 (mm-30) REVERT: R 77 GLN cc_start: 0.8451 (tp40) cc_final: 0.8172 (tp40) REVERT: S 53 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8353 (mm-30) REVERT: T 32 ASP cc_start: 0.6952 (t0) cc_final: 0.6429 (m-30) REVERT: T 53 GLU cc_start: 0.8296 (tp30) cc_final: 0.8091 (mm-30) REVERT: U 32 ASP cc_start: 0.7382 (m-30) cc_final: 0.7043 (m-30) REVERT: V 33 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7284 (mttp) REVERT: V 67 VAL cc_start: 0.8118 (t) cc_final: 0.7840 (t) REVERT: W 32 ASP cc_start: 0.8094 (m-30) cc_final: 0.7879 (m-30) REVERT: W 69 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7648 (tmtt) REVERT: X 33 LYS cc_start: 0.7764 (mtpp) cc_final: 0.7476 (mtmt) REVERT: Y 6 SER cc_start: 0.8200 (m) cc_final: 0.7939 (p) REVERT: Y 80 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.4055 (ttm170) REVERT: Z 32 ASP cc_start: 0.8235 (m-30) cc_final: 0.7788 (m-30) REVERT: a 10 ASP cc_start: 0.7746 (m-30) cc_final: 0.7474 (m-30) REVERT: b 33 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7433 (mttm) REVERT: b 80 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.4804 (mpt180) REVERT: c 53 GLU cc_start: 0.7563 (tp30) cc_final: 0.6891 (mm-30) REVERT: c 61 GLN cc_start: 0.9025 (tt0) cc_final: 0.8732 (tt0) REVERT: d 11 ASP cc_start: 0.8389 (m-30) cc_final: 0.8157 (m-30) outliers start: 23 outliers final: 12 residues processed: 327 average time/residue: 0.2987 time to fit residues: 146.8079 Evaluate side-chains 314 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 295 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain c residue 76 ILE Chi-restraints excluded: chain d residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 0.0980 chunk 166 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 59 ASN d 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.7218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18690 Z= 0.212 Angle : 0.438 9.436 25440 Z= 0.238 Chirality : 0.034 0.110 2910 Planarity : 0.003 0.028 3330 Dihedral : 3.515 31.975 2520 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.06 % Allowed : 12.47 % Favored : 86.46 % 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: 4.54 (0.17), residues: 2280 helix: 3.71 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.52 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Y 5 PHE 0.008 0.001 PHE H 16 TYR 0.016 0.002 TYR G 57 ARG 0.008 0.001 ARG J 80 ********************** REFINEMENT MACRO_CYCLE 10 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 315 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 294 time to evaluate : 2.244 Fit side-chains REVERT: A 80 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7250 (ptt90) REVERT: B 55 ASN cc_start: 0.8374 (t0) cc_final: 0.7988 (t0) REVERT: B 66 LYS cc_start: 0.8205 (tptp) cc_final: 0.6562 (ttmt) REVERT: C 66 LYS cc_start: 0.8676 (tptp) cc_final: 0.6648 (mttt) REVERT: D 3 THR cc_start: 0.7994 (m) cc_final: 0.7782 (t) REVERT: D 37 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7091 (tmtt) REVERT: D 66 LYS cc_start: 0.8087 (tptp) cc_final: 0.6136 (mttm) REVERT: E 37 LYS cc_start: 0.7804 (ttmt) cc_final: 0.6879 (tptt) REVERT: E 66 LYS cc_start: 0.8090 (tptp) cc_final: 0.6234 (ttmt) REVERT: F 37 LYS cc_start: 0.7791 (ttmt) cc_final: 0.6704 (tptt) REVERT: G 32 ASP cc_start: 0.7735 (m-30) cc_final: 0.7515 (m-30) REVERT: G 80 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6994 (ptt90) REVERT: H 80 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.5796 (pmt100) REVERT: I 32 ASP cc_start: 0.7554 (m-30) cc_final: 0.7013 (m-30) REVERT: K 32 ASP cc_start: 0.7584 (m-30) cc_final: 0.7242 (m-30) REVERT: K 80 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.5568 (ptt90) REVERT: L 21 ASP cc_start: 0.8141 (m-30) cc_final: 0.7930 (m-30) REVERT: L 53 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8287 (mm-30) REVERT: L 80 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6316 (pmt100) REVERT: M 53 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8373 (mm-30) REVERT: N 28 THR cc_start: 0.8089 (m) cc_final: 0.7190 (p) REVERT: N 32 ASP cc_start: 0.7747 (m-30) cc_final: 0.7345 (m-30) REVERT: N 57 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8036 (t80) REVERT: O 32 ASP cc_start: 0.7849 (m-30) cc_final: 0.7478 (m-30) REVERT: O 33 LYS cc_start: 0.7891 (mttm) cc_final: 0.7615 (mtmm) REVERT: O 80 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.5394 (pmt100) REVERT: S 53 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8337 (mm-30) REVERT: T 32 ASP cc_start: 0.6966 (t0) cc_final: 0.6466 (m-30) REVERT: T 53 GLU cc_start: 0.8385 (tp30) cc_final: 0.8143 (mm-30) REVERT: U 32 ASP cc_start: 0.7343 (m-30) cc_final: 0.6983 (m-30) REVERT: V 33 LYS cc_start: 0.7650 (mtmm) cc_final: 0.7309 (mttp) REVERT: W 32 ASP cc_start: 0.8131 (m-30) cc_final: 0.7919 (m-30) REVERT: X 33 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7462 (mtmm) REVERT: Y 6 SER cc_start: 0.8221 (m) cc_final: 0.7954 (p) REVERT: Y 80 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.4129 (ttm170) REVERT: Z 32 ASP cc_start: 0.8235 (m-30) cc_final: 0.7774 (m-30) REVERT: a 10 ASP cc_start: 0.7664 (m-30) cc_final: 0.7410 (m-30) REVERT: b 33 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7423 (mttm) REVERT: b 80 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.4720 (mpt180) REVERT: c 53 GLU cc_start: 0.7564 (tp30) cc_final: 0.6904 (mm-30) REVERT: d 11 ASP cc_start: 0.8350 (m-30) cc_final: 0.8084 (m-30) outliers start: 21 outliers final: 11 residues processed: 311 average time/residue: 0.3134 time to fit residues: 145.4730 Evaluate side-chains 311 residues out of total 1980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 291 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain G residue 80 ARG Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain K residue 80 ARG Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 80 ARG Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 80 ARG Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain R residue 6 SER Chi-restraints excluded: chain R residue 79 PHE Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain Y residue 80 ARG Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain d residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 24 optimal weight: 0.0270 chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 0.0770 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 61 GLN L 61 GLN M 61 GLN R 63 ASN V 59 ASN W 63 ASN d 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.079925 restraints weight = 25452.005| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.42 r_work: 0.2724 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 18690 Z= 0.113 Angle : 0.383 9.412 25440 Z= 0.207 Chirality : 0.031 0.106 2910 Planarity : 0.003 0.030 3330 Dihedral : 3.272 27.002 2520 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.91 % Allowed : 12.93 % Favored : 86.16 % 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: 4.90 (0.17), residues: 2280 helix: 3.96 (0.10), residues: 2010 sheet: None (None), residues: 0 loop : -3.57 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP Y 5 PHE 0.005 0.001 PHE O 79 TYR 0.013 0.001 TYR G 57 ARG 0.008 0.000 ARG J 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3625.06 seconds wall clock time: 66 minutes 46.63 seconds (4006.63 seconds total)