Starting phenix.real_space_refine on Sun Jul 21 19:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3r_22656/07_2024/7k3r_22656.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3r_22656/07_2024/7k3r_22656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3r_22656/07_2024/7k3r_22656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3r_22656/07_2024/7k3r_22656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3r_22656/07_2024/7k3r_22656.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3r_22656/07_2024/7k3r_22656.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10332 2.51 5 N 2730 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16170 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "B" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "C" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "D" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "F" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "G" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "H" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "I" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "J" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "K" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "L" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "M" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "N" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "O" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "P" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "Q" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "R" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "S" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "T" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Chain: "U" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 770 Classifications: {'peptide': 95} Link IDs: {'TRANS': 94} Time building chain proxies: 8.10, per 1000 atoms: 0.50 Number of scatterers: 16170 At special positions: 0 Unit cell: (107.58, 107.58, 126.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3024 8.00 N 2730 7.00 C 10332 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: 5.82 Conformation dependent library (CDL) restraints added in 2.4 seconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN A 17 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 18 " --> pdb=" O LEU A 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 14 through 18' Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 75 through 94 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN B 17 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 18 " --> pdb=" O LEU B 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 14 through 18' Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 58 through 73 Processing helix chain 'B' and resid 75 through 94 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN C 17 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 18 " --> pdb=" O LEU C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 14 through 18' Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 58 through 73 Processing helix chain 'C' and resid 75 through 94 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.515A pdb=" N ASN D 17 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 18 " --> pdb=" O LEU D 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 14 through 18' Processing helix chain 'D' and resid 19 through 29 Processing helix chain 'D' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 58 through 73 Processing helix chain 'D' and resid 75 through 94 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN E 17 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE E 18 " --> pdb=" O LEU E 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 14 through 18' Processing helix chain 'E' and resid 19 through 29 Processing helix chain 'E' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 58 through 73 Processing helix chain 'E' and resid 75 through 94 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN F 17 " --> pdb=" O GLY F 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE F 18 " --> pdb=" O LEU F 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 14 through 18' Processing helix chain 'F' and resid 19 through 29 Processing helix chain 'F' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 58 through 73 Processing helix chain 'F' and resid 75 through 94 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.515A pdb=" N ASN G 17 " --> pdb=" O GLY G 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE G 18 " --> pdb=" O LEU G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 18' Processing helix chain 'G' and resid 19 through 29 Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 58 through 73 Processing helix chain 'G' and resid 75 through 94 Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN H 17 " --> pdb=" O GLY H 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 18 " --> pdb=" O LEU H 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 14 through 18' Processing helix chain 'H' and resid 19 through 29 Processing helix chain 'H' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 58 Processing helix chain 'H' and resid 58 through 73 Processing helix chain 'H' and resid 75 through 94 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN I 17 " --> pdb=" O GLY I 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE I 18 " --> pdb=" O LEU I 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 14 through 18' Processing helix chain 'I' and resid 19 through 29 Processing helix chain 'I' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 58 Processing helix chain 'I' and resid 58 through 73 Processing helix chain 'I' and resid 75 through 94 Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN J 17 " --> pdb=" O GLY J 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE J 18 " --> pdb=" O LEU J 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 18' Processing helix chain 'J' and resid 19 through 29 Processing helix chain 'J' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 58 Processing helix chain 'J' and resid 58 through 73 Processing helix chain 'J' and resid 75 through 94 Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN K 17 " --> pdb=" O GLY K 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 18 " --> pdb=" O LEU K 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 14 through 18' Processing helix chain 'K' and resid 19 through 29 Processing helix chain 'K' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 58 Processing helix chain 'K' and resid 58 through 73 Processing helix chain 'K' and resid 75 through 94 Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'L' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L 18 " --> pdb=" O LEU L 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 14 through 18' Processing helix chain 'L' and resid 19 through 29 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU L 41 " --> pdb=" O ALA L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 58 Processing helix chain 'L' and resid 58 through 73 Processing helix chain 'L' and resid 75 through 94 Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN M 17 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE M 18 " --> pdb=" O LEU M 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 14 through 18' Processing helix chain 'M' and resid 19 through 29 Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 58 Processing helix chain 'M' and resid 58 through 73 Processing helix chain 'M' and resid 75 through 94 Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 14 through 18 removed outlier: 3.515A pdb=" N ASN N 17 " --> pdb=" O GLY N 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 18 " --> pdb=" O LEU N 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 14 through 18' Processing helix chain 'N' and resid 19 through 29 Processing helix chain 'N' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU N 41 " --> pdb=" O ALA N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 58 Processing helix chain 'N' and resid 58 through 73 Processing helix chain 'N' and resid 75 through 94 Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'O' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN O 17 " --> pdb=" O GLY O 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE O 18 " --> pdb=" O LEU O 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 14 through 18' Processing helix chain 'O' and resid 19 through 29 Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 58 Processing helix chain 'O' and resid 58 through 73 Processing helix chain 'O' and resid 75 through 94 Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 14 through 18 removed outlier: 3.517A pdb=" N ASN P 17 " --> pdb=" O GLY P 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE P 18 " --> pdb=" O LEU P 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 14 through 18' Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 58 Processing helix chain 'P' and resid 58 through 73 Processing helix chain 'P' and resid 75 through 94 Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'Q' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN Q 17 " --> pdb=" O GLY Q 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE Q 18 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 14 through 18' Processing helix chain 'Q' and resid 19 through 29 Processing helix chain 'Q' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 58 Processing helix chain 'Q' and resid 58 through 73 Processing helix chain 'Q' and resid 75 through 94 Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN R 17 " --> pdb=" O GLY R 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE R 18 " --> pdb=" O LEU R 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 14 through 18' Processing helix chain 'R' and resid 19 through 29 Processing helix chain 'R' and resid 37 through 42 removed outlier: 3.971A pdb=" N LEU R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 58 Processing helix chain 'R' and resid 58 through 73 Processing helix chain 'R' and resid 75 through 94 Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'S' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN S 17 " --> pdb=" O GLY S 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE S 18 " --> pdb=" O LEU S 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 14 through 18' Processing helix chain 'S' and resid 19 through 29 Processing helix chain 'S' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 58 Processing helix chain 'S' and resid 58 through 73 Processing helix chain 'S' and resid 75 through 94 Processing helix chain 'T' and resid 2 through 13 Processing helix chain 'T' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN T 17 " --> pdb=" O GLY T 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE T 18 " --> pdb=" O LEU T 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 14 through 18' Processing helix chain 'T' and resid 19 through 29 Processing helix chain 'T' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU T 41 " --> pdb=" O ALA T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 58 Processing helix chain 'T' and resid 58 through 73 Processing helix chain 'T' and resid 75 through 94 Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'U' and resid 14 through 18 removed outlier: 3.516A pdb=" N ASN U 17 " --> pdb=" O GLY U 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE U 18 " --> pdb=" O LEU U 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 14 through 18' Processing helix chain 'U' and resid 19 through 29 Processing helix chain 'U' and resid 37 through 42 removed outlier: 3.970A pdb=" N LEU U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 58 Processing helix chain 'U' and resid 58 through 73 Processing helix chain 'U' and resid 75 through 94 1135 hydrogen bonds defined for protein. 3405 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: 4.36 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5229 1.34 - 1.46: 2430 1.46 - 1.57: 8511 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 16338 Sorted by residual: bond pdb=" SD MET U 53 " pdb=" CE MET U 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" SD MET N 53 " pdb=" CE MET N 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" SD MET B 53 " pdb=" CE MET B 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" SD MET D 53 " pdb=" CE MET D 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" SD MET Q 53 " pdb=" CE MET Q 53 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 16333 not shown) Histogram of bond angle deviations from ideal: 99.45 - 105.82: 84 105.82 - 112.19: 8195 112.19 - 118.55: 4908 118.55 - 124.92: 8590 124.92 - 131.28: 42 Bond angle restraints: 21819 Sorted by residual: angle pdb=" C LEU R 73 " pdb=" N ASN R 74 " pdb=" CA ASN R 74 " ideal model delta sigma weight residual 122.19 125.92 -3.73 1.41e+00 5.03e-01 6.98e+00 angle pdb=" C LEU O 73 " pdb=" N ASN O 74 " pdb=" CA ASN O 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C LEU N 73 " pdb=" N ASN N 74 " pdb=" CA ASN N 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C LEU H 73 " pdb=" N ASN H 74 " pdb=" CA ASN H 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C LEU M 73 " pdb=" N ASN M 74 " pdb=" CA ASN M 74 " ideal model delta sigma weight residual 122.19 125.91 -3.72 1.41e+00 5.03e-01 6.95e+00 ... (remaining 21814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.68: 8795 9.68 - 19.35: 1180 19.35 - 29.02: 63 29.02 - 38.70: 84 38.70 - 48.37: 42 Dihedral angle restraints: 10164 sinusoidal: 4305 harmonic: 5859 Sorted by residual: dihedral pdb=" CB MET M 76 " pdb=" CG MET M 76 " pdb=" SD MET M 76 " pdb=" CE MET M 76 " ideal model delta sinusoidal sigma weight residual 60.00 108.37 -48.37 3 1.50e+01 4.44e-03 8.63e+00 dihedral pdb=" CB MET T 76 " pdb=" CG MET T 76 " pdb=" SD MET T 76 " pdb=" CE MET T 76 " ideal model delta sinusoidal sigma weight residual 60.00 108.37 -48.37 3 1.50e+01 4.44e-03 8.63e+00 dihedral pdb=" CB MET B 76 " pdb=" CG MET B 76 " pdb=" SD MET B 76 " pdb=" CE MET B 76 " ideal model delta sinusoidal sigma weight residual 60.00 108.36 -48.36 3 1.50e+01 4.44e-03 8.63e+00 ... (remaining 10161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1066 0.024 - 0.048: 669 0.048 - 0.072: 436 0.072 - 0.096: 262 0.096 - 0.120: 87 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA ASN P 74 " pdb=" N ASN P 74 " pdb=" C ASN P 74 " pdb=" CB ASN P 74 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ASN D 74 " pdb=" N ASN D 74 " pdb=" C ASN D 74 " pdb=" CB ASN D 74 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA ASN E 74 " pdb=" N ASN E 74 " pdb=" C ASN E 74 " pdb=" CB ASN E 74 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 2517 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 34 " 0.004 2.00e-02 2.50e+03 9.09e-03 1.45e+00 pdb=" CG PHE C 34 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE C 34 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 34 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 34 " 0.004 2.00e-02 2.50e+03 9.07e-03 1.44e+00 pdb=" CG PHE G 34 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE G 34 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE G 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE G 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE G 34 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 34 " 0.004 2.00e-02 2.50e+03 9.05e-03 1.43e+00 pdb=" CG PHE A 34 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 34 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 34 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 34 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 34 " -0.004 2.00e-02 2.50e+03 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3220 2.76 - 3.30: 15216 3.30 - 3.83: 25692 3.83 - 4.37: 32587 4.37 - 4.90: 56178 Nonbonded interactions: 132893 Sorted by model distance: nonbonded pdb=" O ALA P 62 " pdb=" OG1 THR P 66 " model vdw 2.229 2.440 nonbonded pdb=" O ALA H 62 " pdb=" OG1 THR H 66 " model vdw 2.229 2.440 nonbonded pdb=" O ALA K 62 " pdb=" OG1 THR K 66 " model vdw 2.229 2.440 nonbonded pdb=" O ALA Q 62 " pdb=" OG1 THR Q 66 " model vdw 2.229 2.440 nonbonded pdb=" O ALA B 62 " pdb=" OG1 THR B 66 " model vdw 2.229 2.440 ... (remaining 132888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.690 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.006 0.031 16338 Z= 0.382 Angle : 0.781 4.825 21819 Z= 0.466 Chirality : 0.046 0.120 2520 Planarity : 0.003 0.011 2730 Dihedral : 9.105 48.374 6342 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.15), residues: 1953 helix: -2.60 (0.08), residues: 1449 sheet: None (None), residues: 0 loop : 0.55 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 42 PHE 0.016 0.003 PHE T 34 TYR 0.010 0.002 TYR U 75 ARG 0.004 0.001 ARG G 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1008 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 63 VAL cc_start: 0.9299 (t) cc_final: 0.9085 (t) REVERT: R 63 VAL cc_start: 0.9274 (t) cc_final: 0.9050 (t) REVERT: S 63 VAL cc_start: 0.9307 (t) cc_final: 0.9090 (t) outliers start: 0 outliers final: 0 residues processed: 1008 average time/residue: 0.3603 time to fit residues: 491.1818 Evaluate side-chains 787 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 787 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 GLN G 92 GLN H 55 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN ** M 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN R 71 GLN S 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16338 Z= 0.194 Angle : 0.517 5.814 21819 Z= 0.303 Chirality : 0.041 0.172 2520 Planarity : 0.004 0.024 2730 Dihedral : 4.506 12.497 2121 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.70 % Allowed : 11.00 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 1953 helix: 0.54 (0.12), residues: 1470 sheet: None (None), residues: 0 loop : 1.24 (0.32), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS R 42 PHE 0.008 0.001 PHE K 70 TYR 0.006 0.001 TYR D 75 ARG 0.005 0.001 ARG R 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 839 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6516 (mt-10) REVERT: I 33 GLU cc_start: 0.6743 (tp30) cc_final: 0.6517 (tp30) REVERT: I 68 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.8032 (ttm-80) REVERT: K 76 MET cc_start: 0.8491 (mmm) cc_final: 0.8282 (mmt) REVERT: M 76 MET cc_start: 0.8431 (mmm) cc_final: 0.8094 (mmt) REVERT: N 76 MET cc_start: 0.8414 (mmm) cc_final: 0.8209 (mmt) REVERT: Q 8 GLU cc_start: 0.6751 (mt-10) cc_final: 0.6433 (mt-10) REVERT: Q 86 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8407 (ttpp) outliers start: 30 outliers final: 10 residues processed: 854 average time/residue: 0.3674 time to fit residues: 423.4203 Evaluate side-chains 804 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 794 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain S residue 61 SER Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 71 GLN B 55 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 GLN ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 GLN P 92 GLN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16338 Z= 0.251 Angle : 0.537 5.039 21819 Z= 0.309 Chirality : 0.042 0.167 2520 Planarity : 0.003 0.017 2730 Dihedral : 4.454 15.165 2121 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.53 % Allowed : 15.42 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1953 helix: 1.48 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.48 (0.34), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS R 42 PHE 0.009 0.001 PHE Q 70 TYR 0.009 0.001 TYR G 93 ARG 0.006 0.001 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 820 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 8 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6542 (mt-10) REVERT: G 8 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6629 (mt-10) REVERT: I 68 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.8029 (ttm-80) REVERT: K 76 MET cc_start: 0.8516 (mmm) cc_final: 0.8294 (mmt) REVERT: M 8 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6669 (mt-10) outliers start: 27 outliers final: 12 residues processed: 822 average time/residue: 0.3613 time to fit residues: 399.2516 Evaluate side-chains 809 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 797 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 92 GLN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16338 Z= 0.224 Angle : 0.522 5.997 21819 Z= 0.300 Chirality : 0.041 0.167 2520 Planarity : 0.003 0.026 2730 Dihedral : 4.402 17.028 2121 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.93 % Allowed : 16.84 % Favored : 81.24 % 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: 2.56 (0.20), residues: 1953 helix: 1.83 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.56 (0.35), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 42 PHE 0.006 0.001 PHE Q 70 TYR 0.009 0.001 TYR Q 93 ARG 0.008 0.001 ARG K 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 816 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 33 GLU cc_start: 0.6948 (tp30) cc_final: 0.6599 (tp30) REVERT: I 68 ARG cc_start: 0.8280 (ttp-110) cc_final: 0.8051 (ttm-80) REVERT: J 8 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6608 (mt-10) REVERT: K 76 MET cc_start: 0.8508 (mmm) cc_final: 0.8285 (mmt) REVERT: Q 8 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6526 (mt-10) REVERT: R 8 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6626 (tt0) outliers start: 34 outliers final: 20 residues processed: 820 average time/residue: 0.3609 time to fit residues: 399.8310 Evaluate side-chains 823 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 803 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain R residue 4 SER Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.2980 chunk 163 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16338 Z= 0.230 Angle : 0.533 6.677 21819 Z= 0.306 Chirality : 0.042 0.182 2520 Planarity : 0.003 0.042 2730 Dihedral : 4.406 17.816 2121 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.87 % Allowed : 18.25 % Favored : 79.88 % 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: 2.80 (0.20), residues: 1953 helix: 1.95 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.87 (0.38), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 42 PHE 0.007 0.001 PHE L 29 TYR 0.015 0.001 TYR S 93 ARG 0.010 0.001 ARG N 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 825 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 8 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6502 (mt-10) REVERT: I 68 ARG cc_start: 0.8277 (ttp-110) cc_final: 0.8059 (ttm-80) REVERT: J 8 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6487 (mt-10) REVERT: K 76 MET cc_start: 0.8503 (mmm) cc_final: 0.8281 (mmt) REVERT: P 8 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6674 (tt0) outliers start: 33 outliers final: 22 residues processed: 829 average time/residue: 0.3613 time to fit residues: 404.6377 Evaluate side-chains 831 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 809 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 21 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16338 Z= 0.284 Angle : 0.577 7.396 21819 Z= 0.328 Chirality : 0.043 0.190 2520 Planarity : 0.003 0.022 2730 Dihedral : 4.435 19.430 2121 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.61 % Allowed : 18.42 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.20), residues: 1953 helix: 1.94 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.98 (0.39), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 42 PHE 0.009 0.001 PHE L 29 TYR 0.018 0.001 TYR K 93 ARG 0.009 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 827 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 68 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8058 (ttm-80) REVERT: O 8 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6620 (mt-10) outliers start: 46 outliers final: 34 residues processed: 834 average time/residue: 0.3598 time to fit residues: 406.0031 Evaluate side-chains 842 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 808 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain R residue 34 PHE Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 21 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16338 Z= 0.227 Angle : 0.572 8.274 21819 Z= 0.326 Chirality : 0.042 0.189 2520 Planarity : 0.003 0.028 2730 Dihedral : 4.388 18.569 2121 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.49 % Allowed : 19.67 % Favored : 77.83 % 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: 2.82 (0.20), residues: 1953 helix: 1.92 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 2.04 (0.39), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 42 PHE 0.007 0.001 PHE D 34 TYR 0.008 0.001 TYR T 93 ARG 0.008 0.001 ARG C 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 822 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 68 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.8059 (ttm-80) REVERT: R 65 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8159 (mtpt) outliers start: 44 outliers final: 32 residues processed: 831 average time/residue: 0.3928 time to fit residues: 449.0921 Evaluate side-chains 833 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 801 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain U residue 16 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16338 Z= 0.365 Angle : 0.664 9.049 21819 Z= 0.371 Chirality : 0.046 0.215 2520 Planarity : 0.003 0.043 2730 Dihedral : 4.557 19.775 2121 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.83 % Allowed : 19.56 % Favored : 77.61 % 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: 2.59 (0.20), residues: 1953 helix: 1.79 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.82 (0.37), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 42 PHE 0.013 0.002 PHE R 29 TYR 0.011 0.001 TYR U 75 ARG 0.012 0.001 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 816 time to evaluate : 2.049 Fit side-chains revert: symmetry clash REVERT: I 68 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.8056 (ttm-80) REVERT: L 72 LYS cc_start: 0.8409 (tptm) cc_final: 0.8139 (tptm) outliers start: 50 outliers final: 38 residues processed: 822 average time/residue: 0.3701 time to fit residues: 410.7234 Evaluate side-chains 834 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 796 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain R residue 34 PHE Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 21 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN J 48 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16338 Z= 0.263 Angle : 0.634 9.614 21819 Z= 0.356 Chirality : 0.043 0.190 2520 Planarity : 0.003 0.032 2730 Dihedral : 4.479 20.108 2121 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.44 % Allowed : 20.52 % Favored : 77.04 % 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: 2.60 (0.20), residues: 1953 helix: 1.78 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.87 (0.38), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 42 PHE 0.007 0.001 PHE L 29 TYR 0.020 0.001 TYR K 93 ARG 0.009 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 815 time to evaluate : 2.040 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6842 (mm-30) REVERT: I 68 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.8065 (ttm-80) REVERT: R 93 TYR cc_start: 0.7107 (m-10) cc_final: 0.6858 (m-10) outliers start: 43 outliers final: 36 residues processed: 821 average time/residue: 0.3600 time to fit residues: 401.1291 Evaluate side-chains 838 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 802 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 34 PHE Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain R residue 34 PHE Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 55 GLN Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain U residue 21 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16338 Z= 0.301 Angle : 0.669 9.892 21819 Z= 0.374 Chirality : 0.045 0.198 2520 Planarity : 0.003 0.030 2730 Dihedral : 4.546 20.770 2121 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.55 % Allowed : 20.46 % Favored : 76.98 % 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: 2.46 (0.20), residues: 1953 helix: 1.70 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.77 (0.37), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 42 PHE 0.009 0.001 PHE R 29 TYR 0.018 0.001 TYR K 93 ARG 0.008 0.001 ARG F 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 805 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 68 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.8059 (ttm-80) outliers start: 45 outliers final: 37 residues processed: 811 average time/residue: 0.3558 time to fit residues: 390.3444 Evaluate side-chains 838 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 801 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain M residue 16 ASP Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain O residue 16 ASP Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain P residue 34 PHE Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain R residue 34 PHE Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 55 GLN Chi-restraints excluded: chain S residue 16 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 16 ASP Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 21 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 GLN J 48 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 74 ASN U 71 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073202 restraints weight = 33869.144| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.42 r_work: 0.2913 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16338 Z= 0.256 Angle : 0.649 10.012 21819 Z= 0.364 Chirality : 0.043 0.196 2520 Planarity : 0.003 0.029 2730 Dihedral : 4.536 20.039 2121 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.32 % Allowed : 20.80 % Favored : 76.87 % 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: 2.46 (0.20), residues: 1953 helix: 1.68 (0.13), residues: 1470 sheet: None (None), residues: 0 loop : 1.83 (0.38), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 42 PHE 0.008 0.001 PHE D 34 TYR 0.010 0.001 TYR S 93 ARG 0.008 0.001 ARG C 81 =============================================================================== Job complete usr+sys time: 6534.58 seconds wall clock time: 115 minutes 8.16 seconds (6908.16 seconds total)