Starting phenix.real_space_refine on Sat Jan 20 00:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7i_22700/01_2024/7k7i_22700.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7i_22700/01_2024/7k7i_22700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7i_22700/01_2024/7k7i_22700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7i_22700/01_2024/7k7i_22700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7i_22700/01_2024/7k7i_22700.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7i_22700/01_2024/7k7i_22700.pdb" } resolution = 3.13 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= 0.000 sd= 0.001 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 55 5.16 5 C 8355 2.51 5 N 2210 2.21 5 O 2575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 24": "OE1" <-> "OE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "H GLU 41": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 81": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 45": "OE1" <-> "OE2" Residue "X TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13195 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "D" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "K" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "J" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Y" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "X" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Time building chain proxies: 7.06, per 1000 atoms: 0.54 Number of scatterers: 13195 At special positions: 0 Unit cell: (129.48, 126.99, 80.51, 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 55 16.00 O 2575 8.00 N 2210 7.00 C 8355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 133 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 133 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 95 " distance=2.02 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 21 " - pdb=" SG CYS M 95 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 21 " - pdb=" SG CYS P 95 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 21 " - pdb=" SG CYS X 95 " distance=2.03 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: 4.95 Conformation dependent library (CDL) restraints added in 2.4 seconds 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 44 sheets defined 6.5% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 82 through 96 removed outlier: 4.105A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.916A pdb=" N THR A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 117' Processing helix chain 'B' and resid 82 through 96 removed outlier: 4.100A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.607A pdb=" N PHE B 117 " --> pdb=" O PHE B 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 removed outlier: 4.288A pdb=" N GLN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.877A pdb=" N THR C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 117' Processing helix chain 'D' and resid 82 through 96 removed outlier: 4.341A pdb=" N GLN D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.594A pdb=" N PHE D 117 " --> pdb=" O PHE D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 removed outlier: 4.091A pdb=" N GLN E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 3.657A pdb=" N PHE E 117 " --> pdb=" O PHE E 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 102 removed outlier: 3.600A pdb=" N SER J 102 " --> pdb=" O TYR J 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 removed outlier: 3.527A pdb=" N ALA A 69 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 52 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A 44 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS A 54 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A 42 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 56 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP A 36 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 99 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 124 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 72 removed outlier: 3.641A pdb=" N ALA B 69 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 56 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL B 58 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE B 39 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 36 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL B 99 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 124 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.835A pdb=" N THR C 57 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 69 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 55 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 56 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 58 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE C 39 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 102 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 124 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N VAL C 123 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN D 46 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 44 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU D 42 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE D 39 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL D 58 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 56 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 55 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 69 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.835A pdb=" N THR C 57 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 69 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 55 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 56 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 58 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE C 39 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR C 33 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 103 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER C 35 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE C 101 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 102 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 124 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N VAL C 123 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN D 46 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 44 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU D 42 " --> pdb=" O SER C 127 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR D 33 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 103 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER D 35 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 101 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY D 124 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.503A pdb=" N ALA E 69 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 56 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL E 58 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE E 39 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TYR E 33 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL E 103 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER E 35 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 101 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY E 124 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.201A pdb=" N LEU L 11 " --> pdb=" O GLY L 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.731A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE L 33 " --> pdb=" O GLN L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AB2, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AB4, first strand: chain 'H' and resid 38 through 39 removed outlier: 3.818A pdb=" N ARG H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.529A pdb=" N TYR H 58 " --> pdb=" O THR H 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.135A pdb=" N LEU K 11 " --> pdb=" O GLY K 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'K' and resid 35 through 36 removed outlier: 6.675A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AC2, first strand: chain 'J' and resid 16 through 19 removed outlier: 3.623A pdb=" N LEU J 17 " --> pdb=" O MET J 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.765A pdb=" N VAL J 96 " --> pdb=" O SER J 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.209A pdb=" N LEU N 11 " --> pdb=" O GLY N 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AC8, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.642A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 16 through 18 removed outlier: 3.705A pdb=" N LEU M 17 " --> pdb=" O MET M 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.256A pdb=" N LEU Q 11 " --> pdb=" O GLY Q 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 19 through 20 Processing sheet with id=AD5, first strand: chain 'Q' and resid 33 through 35 removed outlier: 3.515A pdb=" N HIS Q 34 " --> pdb=" O GLN Q 89 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 48 through 49 Processing sheet with id=AD7, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'P' and resid 10 through 11 Processing sheet with id=AD9, first strand: chain 'P' and resid 17 through 18 Processing sheet with id=AE1, first strand: chain 'P' and resid 45 through 47 removed outlier: 6.838A pdb=" N CYS P 95 " --> pdb=" O TRP P 110 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TRP P 110 " --> pdb=" O CYS P 95 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ARG P 97 " --> pdb=" O ASP P 108 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 49 through 50 Processing sheet with id=AE3, first strand: chain 'Y' and resid 4 through 6 Processing sheet with id=AE4, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.119A pdb=" N LEU Y 11 " --> pdb=" O GLY Y 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Y' and resid 19 through 20 Processing sheet with id=AE6, first strand: chain 'Y' and resid 35 through 36 removed outlier: 6.754A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 18 through 19 Processing sheet with id=AE8, first strand: chain 'X' and resid 57 through 58 removed outlier: 6.681A pdb=" N TRP X 35 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER X 34 " --> pdb=" O VAL X 96 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 660 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: 3.42 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4189 1.34 - 1.46: 3704 1.46 - 1.58: 5582 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 13545 Sorted by residual: bond pdb=" CA ASN H 104 " pdb=" C ASN H 104 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.38e-02 5.25e+03 1.81e+00 bond pdb=" N TYR H 105 " pdb=" CA TYR H 105 " ideal model delta sigma weight residual 1.455 1.469 -0.015 1.36e-02 5.41e+03 1.15e+00 bond pdb=" CB CYS J 95 " pdb=" SG CYS J 95 " ideal model delta sigma weight residual 1.808 1.775 0.033 3.30e-02 9.18e+02 9.84e-01 bond pdb=" CA ILE N 83 " pdb=" CB ILE N 83 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.74e-01 bond pdb=" C VAL B 67 " pdb=" N VAL B 68 " ideal model delta sigma weight residual 1.330 1.320 0.010 1.42e-02 4.96e+03 5.18e-01 ... (remaining 13540 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.65: 377 106.65 - 113.50: 7196 113.50 - 120.35: 4681 120.35 - 127.20: 5982 127.20 - 134.05: 179 Bond angle restraints: 18415 Sorted by residual: angle pdb=" C ASN J 73 " pdb=" N ALA J 74 " pdb=" CA ALA J 74 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N VAL M 47 " pdb=" CA VAL M 47 " pdb=" C VAL M 47 " ideal model delta sigma weight residual 109.34 115.20 -5.86 2.08e+00 2.31e-01 7.92e+00 angle pdb=" C TYR K 50 " pdb=" N ALA K 51 " pdb=" CA ALA K 51 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.56e+00 angle pdb=" N ALA M 48 " pdb=" CA ALA M 48 " pdb=" C ALA M 48 " ideal model delta sigma weight residual 110.06 113.90 -3.84 1.43e+00 4.89e-01 7.19e+00 angle pdb=" N GLY J 25 " pdb=" CA GLY J 25 " pdb=" C GLY J 25 " ideal model delta sigma weight residual 113.18 118.79 -5.61 2.37e+00 1.78e-01 5.61e+00 ... (remaining 18410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7165 18.00 - 36.00: 616 36.00 - 54.01: 93 54.01 - 72.01: 7 72.01 - 90.01: 4 Dihedral angle restraints: 7885 sinusoidal: 3000 harmonic: 4885 Sorted by residual: dihedral pdb=" CB CYS J 21 " pdb=" SG CYS J 21 " pdb=" SG CYS J 95 " pdb=" CB CYS J 95 " ideal model delta sinusoidal sigma weight residual -86.00 -176.01 90.01 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS Y 23 " pdb=" SG CYS Y 23 " pdb=" SG CYS Y 88 " pdb=" CB CYS Y 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.60 -62.60 1 1.00e+01 1.00e-02 5.18e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 149.70 -56.70 1 1.00e+01 1.00e-02 4.33e+01 ... (remaining 7882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1221 0.032 - 0.063: 500 0.063 - 0.095: 143 0.095 - 0.127: 106 0.127 - 0.159: 5 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CB THR X 68 " pdb=" CA THR X 68 " pdb=" OG1 THR X 68 " pdb=" CG2 THR X 68 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA VAL H 47 " pdb=" N VAL H 47 " pdb=" C VAL H 47 " pdb=" CB VAL H 47 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE M 50 " pdb=" N ILE M 50 " pdb=" C ILE M 50 " pdb=" CB ILE M 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1972 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 39 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO J 40 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO J 40 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 40 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 39 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO M 40 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO M 40 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO M 40 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 99 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" C TYR M 99 " -0.021 2.00e-02 2.50e+03 pdb=" O TYR M 99 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR M 100 " 0.007 2.00e-02 2.50e+03 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1530 2.75 - 3.29: 12848 3.29 - 3.82: 21017 3.82 - 4.36: 25380 4.36 - 4.90: 45448 Nonbonded interactions: 106223 Sorted by model distance: nonbonded pdb=" O ARG M 66 " pdb=" OG SER M 83 " model vdw 2.211 2.440 nonbonded pdb=" OE1 GLU E 24 " pdb=" OH TYR X 100 " model vdw 2.222 2.440 nonbonded pdb=" O ARG H 66 " pdb=" OG SER H 83 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.239 2.440 nonbonded pdb=" OE1 GLU C 37 " pdb=" OG1 THR C 57 " model vdw 2.242 2.440 ... (remaining 106218 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' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'Q' selection = chain 'Y' } 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: 3.260 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: 13.590 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 35.660 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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 : 0.003 0.033 13545 Z= 0.194 Angle : 0.550 6.818 18415 Z= 0.307 Chirality : 0.042 0.159 1975 Planarity : 0.003 0.034 2350 Dihedral : 12.848 81.122 4735 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -5.32 (0.16), residues: 1675 helix: -3.91 (0.29), residues: 75 sheet: -3.64 (0.18), residues: 585 loop : -3.55 (0.15), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 110 HIS 0.005 0.001 HIS C 43 PHE 0.008 0.001 PHE D 117 TYR 0.011 0.001 TYR X 99 ARG 0.003 0.000 ARG J 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.595 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: symmetry clash REVERT: L 69 THR cc_start: 0.8725 (p) cc_final: 0.7088 (p) REVERT: L 82 ASP cc_start: 0.8033 (m-30) cc_final: 0.7091 (m-30) REVERT: L 85 ASP cc_start: 0.7836 (m-30) cc_final: 0.7143 (m-30) REVERT: H 72 ASP cc_start: 0.7141 (t70) cc_final: 0.6469 (t0) REVERT: K 69 THR cc_start: 0.8647 (p) cc_final: 0.8310 (m) REVERT: K 85 ASP cc_start: 0.7948 (m-30) cc_final: 0.7299 (m-30) REVERT: J 72 ASP cc_start: 0.7648 (t0) cc_final: 0.7255 (t0) REVERT: N 76 ASN cc_start: 0.8053 (p0) cc_final: 0.7714 (p0) REVERT: N 82 ASP cc_start: 0.8084 (m-30) cc_final: 0.7644 (m-30) REVERT: M 49 THR cc_start: 0.8035 (m) cc_final: 0.7798 (m) REVERT: Q 69 THR cc_start: 0.8592 (p) cc_final: 0.8085 (m) REVERT: Q 76 ASN cc_start: 0.8184 (p0) cc_final: 0.7586 (p0) REVERT: Q 82 ASP cc_start: 0.7747 (m-30) cc_final: 0.6453 (m-30) REVERT: P 31 TYR cc_start: 0.7608 (m-80) cc_final: 0.7207 (m-80) REVERT: Y 75 ILE cc_start: 0.7703 (mt) cc_final: 0.7485 (mt) REVERT: X 45 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7126 (mt-10) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.3244 time to fit residues: 169.8408 Evaluate side-chains 292 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN C 120 ASN D 120 ASN L 37 GLN L 49 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN M 98 GLN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN ** Y 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN X 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 13545 Z= 0.583 Angle : 0.769 10.418 18415 Z= 0.402 Chirality : 0.048 0.154 1975 Planarity : 0.005 0.044 2350 Dihedral : 5.236 31.704 1860 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer: Outliers : 2.48 % Allowed : 16.97 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.49 (0.18), residues: 1675 helix: -1.16 (0.54), residues: 80 sheet: -3.24 (0.19), residues: 585 loop : -3.06 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 46 HIS 0.008 0.002 HIS K 90 PHE 0.024 0.002 PHE H 67 TYR 0.035 0.002 TYR X 109 ARG 0.012 0.001 ARG P 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 307 time to evaluate : 1.727 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 ASN cc_start: 0.5548 (p0) cc_final: 0.5263 (p0) REVERT: L 24 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6989 (mmm160) REVERT: L 85 ASP cc_start: 0.7507 (m-30) cc_final: 0.7165 (m-30) REVERT: J 72 ASP cc_start: 0.8086 (t0) cc_final: 0.7408 (t0) REVERT: M 49 THR cc_start: 0.8379 (m) cc_final: 0.8160 (m) REVERT: M 97 ARG cc_start: 0.6214 (ptp-170) cc_final: 0.5576 (ptp-170) REVERT: P 31 TYR cc_start: 0.8100 (m-80) cc_final: 0.7720 (m-80) REVERT: P 77 THR cc_start: 0.8399 (p) cc_final: 0.8117 (p) REVERT: P 97 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7763 (ptt90) REVERT: Y 24 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7140 (mtm-85) REVERT: X 45 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7423 (mt-10) outliers start: 36 outliers final: 25 residues processed: 325 average time/residue: 0.3200 time to fit residues: 140.6180 Evaluate side-chains 291 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 264 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 3 LEU Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 102 ASP Chi-restraints excluded: chain P residue 6 SER Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 6 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN C 120 ASN D 120 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN Q 37 GLN Y 37 GLN Y 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13545 Z= 0.206 Angle : 0.624 8.890 18415 Z= 0.319 Chirality : 0.044 0.159 1975 Planarity : 0.004 0.052 2350 Dihedral : 4.872 27.555 1860 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.34 % Allowed : 19.72 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -4.04 (0.18), residues: 1675 helix: -0.44 (0.55), residues: 80 sheet: -2.91 (0.19), residues: 625 loop : -2.77 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 46 HIS 0.009 0.001 HIS L 90 PHE 0.016 0.001 PHE H 67 TYR 0.012 0.001 TYR X 31 ARG 0.009 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 299 time to evaluate : 1.550 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 72 ASP cc_start: 0.7991 (t0) cc_final: 0.7379 (t0) REVERT: J 109 TYR cc_start: 0.6877 (p90) cc_final: 0.6378 (p90) REVERT: M 43 ARG cc_start: 0.7061 (ptm-80) cc_final: 0.6804 (ptm-80) REVERT: M 45 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6743 (mt-10) REVERT: Q 103 HIS cc_start: 0.6903 (OUTLIER) cc_final: 0.6394 (m-70) REVERT: X 72 ASP cc_start: 0.7223 (t0) cc_final: 0.6805 (t0) REVERT: X 75 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7380 (mtp85) outliers start: 34 outliers final: 19 residues processed: 315 average time/residue: 0.3326 time to fit residues: 140.0575 Evaluate side-chains 283 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 263 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.0980 chunk 109 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN L 49 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** X 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13545 Z= 0.268 Angle : 0.622 7.782 18415 Z= 0.319 Chirality : 0.044 0.146 1975 Planarity : 0.004 0.082 2350 Dihedral : 4.854 27.603 1860 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 2.62 % Allowed : 19.17 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.81 (0.19), residues: 1675 helix: 0.25 (0.57), residues: 80 sheet: -2.70 (0.18), residues: 695 loop : -2.63 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 46 HIS 0.012 0.001 HIS N 90 PHE 0.017 0.001 PHE M 26 TYR 0.023 0.001 TYR X 31 ARG 0.010 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 287 time to evaluate : 1.802 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: symmetry clash revert: symmetry clash REVERT: L 103 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6612 (m-70) REVERT: J 72 ASP cc_start: 0.8043 (t0) cc_final: 0.7453 (t0) REVERT: M 45 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6734 (mt-10) REVERT: Q 103 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6330 (m-70) REVERT: X 43 ARG cc_start: 0.6816 (ttp80) cc_final: 0.6497 (tmm-80) REVERT: X 72 ASP cc_start: 0.7319 (t0) cc_final: 0.6871 (t0) REVERT: X 75 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7348 (mtp85) outliers start: 38 outliers final: 26 residues processed: 302 average time/residue: 0.3311 time to fit residues: 134.7628 Evaluate side-chains 292 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 264 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 120 ASN E 120 ASN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13545 Z= 0.551 Angle : 0.747 11.702 18415 Z= 0.389 Chirality : 0.047 0.184 1975 Planarity : 0.005 0.081 2350 Dihedral : 5.298 26.950 1860 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 3.59 % Allowed : 20.90 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.72 (0.19), residues: 1675 helix: 0.47 (0.56), residues: 80 sheet: -2.53 (0.18), residues: 710 loop : -2.69 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 46 HIS 0.007 0.002 HIS L 90 PHE 0.016 0.002 PHE H 67 TYR 0.023 0.002 TYR H 99 ARG 0.010 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 266 time to evaluate : 1.641 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 MET cc_start: 0.8317 (mmm) cc_final: 0.8096 (mtp) REVERT: K 89 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: J 72 ASP cc_start: 0.8100 (t0) cc_final: 0.7285 (t0) REVERT: N 4 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6704 (mm) REVERT: M 49 THR cc_start: 0.8445 (m) cc_final: 0.8227 (m) outliers start: 52 outliers final: 41 residues processed: 294 average time/residue: 0.3577 time to fit residues: 141.2792 Evaluate side-chains 292 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 249 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 49 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 29 ILE Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 85 ASP Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13545 Z= 0.240 Angle : 0.631 8.154 18415 Z= 0.323 Chirality : 0.044 0.220 1975 Planarity : 0.004 0.060 2350 Dihedral : 5.005 25.674 1860 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 3.31 % Allowed : 21.59 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.52 (0.19), residues: 1675 helix: 0.75 (0.57), residues: 80 sheet: -2.39 (0.18), residues: 730 loop : -2.56 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 46 HIS 0.009 0.001 HIS N 90 PHE 0.015 0.001 PHE H 67 TYR 0.029 0.001 TYR H 99 ARG 0.011 0.001 ARG J 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 274 time to evaluate : 1.726 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 103 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6598 (m-70) REVERT: H 33 MET cc_start: 0.8262 (mmm) cc_final: 0.8059 (mtp) REVERT: K 89 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: J 72 ASP cc_start: 0.7940 (t0) cc_final: 0.7450 (t0) REVERT: N 79 GLU cc_start: 0.8373 (mp0) cc_final: 0.8172 (mp0) REVERT: M 37 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7949 (ptp-170) REVERT: M 49 THR cc_start: 0.8092 (m) cc_final: 0.7851 (m) REVERT: Q 82 ASP cc_start: 0.7875 (m-30) cc_final: 0.7639 (m-30) REVERT: Q 103 HIS cc_start: 0.6961 (OUTLIER) cc_final: 0.6475 (m-70) REVERT: X 72 ASP cc_start: 0.7131 (t0) cc_final: 0.6679 (t0) outliers start: 48 outliers final: 36 residues processed: 297 average time/residue: 0.3432 time to fit residues: 136.2987 Evaluate side-chains 299 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 259 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 89 GLN Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 ASN L 49 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 GLN ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13545 Z= 0.173 Angle : 0.616 7.135 18415 Z= 0.317 Chirality : 0.044 0.167 1975 Planarity : 0.004 0.049 2350 Dihedral : 4.749 23.506 1860 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.62 % Allowed : 22.21 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.22 (0.19), residues: 1675 helix: 0.97 (0.58), residues: 80 sheet: -2.11 (0.19), residues: 730 loop : -2.43 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 46 HIS 0.011 0.001 HIS N 90 PHE 0.013 0.001 PHE J 26 TYR 0.010 0.001 TYR X 79 ARG 0.015 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 281 time to evaluate : 1.943 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 103 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6616 (m-70) REVERT: J 45 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6920 (mt-10) REVERT: J 72 ASP cc_start: 0.7942 (t0) cc_final: 0.7596 (t0) REVERT: J 96 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8103 (m) REVERT: M 37 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7769 (ptp-170) REVERT: M 49 THR cc_start: 0.7964 (m) cc_final: 0.7753 (m) REVERT: M 100 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7445 (m-10) REVERT: Q 103 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6458 (m-70) outliers start: 38 outliers final: 26 residues processed: 297 average time/residue: 0.3468 time to fit residues: 137.1489 Evaluate side-chains 283 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 ASN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13545 Z= 0.381 Angle : 0.694 9.809 18415 Z= 0.359 Chirality : 0.046 0.194 1975 Planarity : 0.005 0.055 2350 Dihedral : 5.055 24.794 1860 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Rotamer: Outliers : 3.24 % Allowed : 22.76 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.20 (0.20), residues: 1675 helix: 1.13 (0.57), residues: 80 sheet: -2.14 (0.19), residues: 740 loop : -2.39 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 46 HIS 0.008 0.002 HIS N 90 PHE 0.013 0.001 PHE H 67 TYR 0.029 0.001 TYR H 99 ARG 0.013 0.001 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 1.677 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: symmetry clash REVERT: L 103 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6671 (m-70) REVERT: J 45 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: J 72 ASP cc_start: 0.7986 (t0) cc_final: 0.7699 (t0) REVERT: M 37 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7865 (ptp-170) REVERT: M 100 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: Q 103 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6547 (m-70) outliers start: 47 outliers final: 40 residues processed: 271 average time/residue: 0.3555 time to fit residues: 128.1924 Evaluate side-chains 289 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 244 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 96 VAL Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13545 Z= 0.243 Angle : 0.660 8.764 18415 Z= 0.337 Chirality : 0.045 0.200 1975 Planarity : 0.004 0.058 2350 Dihedral : 4.949 25.455 1860 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 2.76 % Allowed : 23.93 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -3.07 (0.20), residues: 1675 helix: 1.23 (0.59), residues: 80 sheet: -1.98 (0.20), residues: 730 loop : -2.39 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 46 HIS 0.008 0.001 HIS N 90 PHE 0.021 0.001 PHE X 67 TYR 0.025 0.001 TYR H 99 ARG 0.014 0.001 ARG M 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 1.736 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: symmetry clash REVERT: A 65 THR cc_start: 0.6812 (OUTLIER) cc_final: 0.6585 (p) REVERT: L 18 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7585 (mmm160) REVERT: L 103 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6651 (m-70) REVERT: J 72 ASP cc_start: 0.7962 (t0) cc_final: 0.7627 (t0) REVERT: M 37 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7814 (ptp-170) REVERT: M 49 THR cc_start: 0.8103 (m) cc_final: 0.7896 (m) REVERT: M 100 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: Q 103 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6476 (m-70) REVERT: Y 24 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6445 (mtm-85) outliers start: 40 outliers final: 33 residues processed: 273 average time/residue: 0.3689 time to fit residues: 133.6463 Evaluate side-chains 281 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 112 GLN Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 GLN ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13545 Z= 0.368 Angle : 0.706 8.153 18415 Z= 0.364 Chirality : 0.046 0.206 1975 Planarity : 0.004 0.059 2350 Dihedral : 5.144 26.880 1860 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.18 % Favored : 87.82 % Rotamer: Outliers : 2.97 % Allowed : 23.93 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.99 (0.20), residues: 1675 helix: 1.21 (0.57), residues: 80 sheet: -1.91 (0.20), residues: 695 loop : -2.34 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 46 HIS 0.009 0.002 HIS N 90 PHE 0.022 0.002 PHE X 67 TYR 0.028 0.001 TYR H 99 ARG 0.014 0.001 ARG J 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3350 Ramachandran restraints generated. 1675 Oldfield, 0 Emsley, 1675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 245 time to evaluate : 1.724 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: symmetry clash REVERT: L 103 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6686 (m-70) REVERT: H 33 MET cc_start: 0.8295 (mmm) cc_final: 0.8093 (mtp) REVERT: K 24 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7058 (mmp80) REVERT: J 72 ASP cc_start: 0.7981 (t0) cc_final: 0.7682 (t0) REVERT: J 86 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7270 (mtm110) REVERT: M 37 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7843 (ptp-170) REVERT: M 100 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7938 (m-10) REVERT: Q 103 HIS cc_start: 0.6839 (OUTLIER) cc_final: 0.6460 (m-70) REVERT: Y 24 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6570 (mtm-85) outliers start: 43 outliers final: 37 residues processed: 265 average time/residue: 0.3517 time to fit residues: 124.0772 Evaluate side-chains 279 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 HIS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 102 ASP Chi-restraints excluded: chain K residue 103 HIS Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain M residue 4 VAL Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 37 ARG Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 100 TYR Chi-restraints excluded: chain Q residue 5 THR Chi-restraints excluded: chain Q residue 90 HIS Chi-restraints excluded: chain Q residue 103 HIS Chi-restraints excluded: chain P residue 43 ARG Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 62 ILE Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 108 ASP Chi-restraints excluded: chain Y residue 72 THR Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 62 ILE Chi-restraints excluded: chain X residue 112 GLN Chi-restraints excluded: chain X residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.0000 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 120 ASN L 49 GLN ** L 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.073202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057180 restraints weight = 41424.805| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.96 r_work: 0.3030 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13545 Z= 0.194 Angle : 0.670 12.078 18415 Z= 0.338 Chirality : 0.046 0.396 1975 Planarity : 0.004 0.058 2350 Dihedral : 4.928 27.420 1860 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 2.41 % Allowed : 24.41 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.91 (0.20), residues: 1675 helix: 1.30 (0.58), residues: 80 sheet: -1.79 (0.20), residues: 730 loop : -2.36 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 46 HIS 0.008 0.001 HIS N 90 PHE 0.018 0.001 PHE X 67 TYR 0.025 0.001 TYR H 99 ARG 0.014 0.001 ARG M 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.42 seconds wall clock time: 66 minutes 12.18 seconds (3972.18 seconds total)