Starting phenix.real_space_refine on Thu Feb 15 23:32:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghs_40049/02_2024/8ghs_40049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghs_40049/02_2024/8ghs_40049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghs_40049/02_2024/8ghs_40049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghs_40049/02_2024/8ghs_40049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghs_40049/02_2024/8ghs_40049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ghs_40049/02_2024/8ghs_40049.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 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 60 5.16 5 C 8911 2.51 5 N 2252 2.21 5 O 2503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 2": "OD1" <-> "OD2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ASP 29": "OD1" <-> "OD2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "D ASP 2": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "F ASP 4": "OD1" <-> "OD2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 29": "OD1" <-> "OD2" Residue "G ASP 32": "OD1" <-> "OD2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 2": "OD1" <-> "OD2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 77": "OE1" <-> "OE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 117": "OE1" <-> "OE2" Residue "L ASP 2": "OD1" <-> "OD2" Residue "L ASP 29": "OD1" <-> "OD2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 2": "OD1" <-> "OD2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1163 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 12, 'TRANS': 133} Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "C" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "F" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1163 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 12, 'TRANS': 133} Chain: "E" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "H" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1188 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "G" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "J" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "I" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "L" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "K" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Time building chain proxies: 7.51, per 1000 atoms: 0.55 Number of scatterers: 13726 At special positions: 0 Unit cell: (180.42, 180.42, 73.72, 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 60 16.00 O 2503 8.00 N 2252 7.00 C 8911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS C 61 " distance=2.04 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS E 61 " distance=2.05 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS I 61 " distance=2.04 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS K 61 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.832A pdb=" N GLU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 removed outlier: 3.723A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.720A pdb=" N THR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 111 removed outlier: 3.654A pdb=" N VAL B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.886A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 12 through 18 removed outlier: 3.515A pdb=" N PHE A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 removed outlier: 7.432A pdb=" N ASP A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.932A pdb=" N THR A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.694A pdb=" N ARG A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.737A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 removed outlier: 4.017A pdb=" N GLU D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 9 " --> pdb=" O PRO D 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 9' Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 26 through 44 removed outlier: 4.153A pdb=" N THR D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.765A pdb=" N THR D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 111 removed outlier: 3.789A pdb=" N ARG D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.939A pdb=" N THR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.796A pdb=" N GLU C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE C 9 " --> pdb=" O PRO C 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 9' Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 26 through 44 removed outlier: 7.145A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.671A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 111 removed outlier: 3.759A pdb=" N ARG C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.936A pdb=" N GLU F 8 " --> pdb=" O PRO F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 26 through 44 removed outlier: 8.540A pdb=" N ASP F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.649A pdb=" N THR F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 111 removed outlier: 3.681A pdb=" N ARG F 82 " --> pdb=" O ASP F 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.656A pdb=" N THR F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 4.114A pdb=" N PHE E 9 " --> pdb=" O PRO E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 removed outlier: 3.546A pdb=" N PHE E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.699A pdb=" N THR E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 76 removed outlier: 3.647A pdb=" N THR E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 111 removed outlier: 3.842A pdb=" N VAL E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 Processing helix chain 'H' and resid 4 through 9 removed outlier: 3.720A pdb=" N GLU H 8 " --> pdb=" O PRO H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 17 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 38 through 44 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.714A pdb=" N THR H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 111 removed outlier: 4.494A pdb=" N VAL H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY H 94 " --> pdb=" O ASN H 90 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 144 through 148 removed outlier: 4.008A pdb=" N ALA H 148 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 3.701A pdb=" N GLU G 8 " --> pdb=" O PRO G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 26 through 44 removed outlier: 3.657A pdb=" N ARG G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.895A pdb=" N THR G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 removed outlier: 3.987A pdb=" N ASN G 90 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.756A pdb=" N LYS G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 128 removed outlier: 3.543A pdb=" N ARG G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 26 through 44 removed outlier: 7.369A pdb=" N ASP J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.888A pdb=" N THR J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 111 removed outlier: 3.835A pdb=" N ARG J 82 " --> pdb=" O ASP J 78 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL J 93 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 removed outlier: 3.515A pdb=" N VAL J 115 " --> pdb=" O GLY J 111 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 128 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.740A pdb=" N GLU I 8 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 26 through 44 removed outlier: 6.999A pdb=" N ASP I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 76 removed outlier: 3.862A pdb=" N THR I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 111 removed outlier: 4.051A pdb=" N VAL I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 removed outlier: 4.291A pdb=" N GLU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 8 removed outlier: 3.826A pdb=" N GLU L 8 " --> pdb=" O PRO L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 17 Processing helix chain 'L' and resid 26 through 44 removed outlier: 3.881A pdb=" N THR L 33 " --> pdb=" O ASP L 29 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.630A pdb=" N THR L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 111 removed outlier: 3.943A pdb=" N VAL L 93 " --> pdb=" O VAL L 89 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS L 96 " --> pdb=" O ASN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.652A pdb=" N THR L 128 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 4.130A pdb=" N PHE K 9 " --> pdb=" O PRO K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'K' and resid 26 through 44 removed outlier: 7.003A pdb=" N ASP K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 76 removed outlier: 3.901A pdb=" N THR K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 111 removed outlier: 3.646A pdb=" N VAL K 93 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY K 94 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 removed outlier: 3.532A pdb=" N VAL K 115 " --> pdb=" O GLY K 111 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG K 127 " --> pdb=" O GLY K 123 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2712 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: 3.65 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4356 1.35 - 1.47: 3623 1.47 - 1.59: 6087 1.59 - 1.72: 0 1.72 - 1.84: 84 Bond restraints: 14150 Sorted by residual: bond pdb=" CA LEU I 140 " pdb=" C LEU I 140 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.42e-02 4.96e+03 1.33e+01 bond pdb=" CA SER I 141 " pdb=" C SER I 141 " ideal model delta sigma weight residual 1.520 1.488 0.031 1.16e-02 7.43e+03 7.36e+00 bond pdb=" CA ASN D 136 " pdb=" CB ASN D 136 " ideal model delta sigma weight residual 1.525 1.564 -0.039 1.47e-02 4.63e+03 7.16e+00 bond pdb=" CA ASN J 136 " pdb=" CB ASN J 136 " ideal model delta sigma weight residual 1.526 1.567 -0.041 1.53e-02 4.27e+03 7.13e+00 bond pdb=" CA LEU F 140 " pdb=" C LEU F 140 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.30e-02 5.92e+03 5.66e+00 ... (remaining 14145 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.57: 632 106.57 - 113.45: 7666 113.45 - 120.34: 5492 120.34 - 127.23: 5331 127.23 - 134.11: 284 Bond angle restraints: 19405 Sorted by residual: angle pdb=" N LEU I 140 " pdb=" CA LEU I 140 " pdb=" C LEU I 140 " ideal model delta sigma weight residual 109.96 99.68 10.28 1.49e+00 4.50e-01 4.76e+01 angle pdb=" N GLY I 123 " pdb=" CA GLY I 123 " pdb=" C GLY I 123 " ideal model delta sigma weight residual 115.08 108.54 6.54 1.19e+00 7.06e-01 3.02e+01 angle pdb=" N ALA H 137 " pdb=" CA ALA H 137 " pdb=" C ALA H 137 " ideal model delta sigma weight residual 110.24 117.80 -7.56 1.46e+00 4.69e-01 2.68e+01 angle pdb=" N ALA H 147 " pdb=" CA ALA H 147 " pdb=" C ALA H 147 " ideal model delta sigma weight residual 112.24 106.25 5.99 1.28e+00 6.10e-01 2.19e+01 angle pdb=" N THR H 142 " pdb=" CA THR H 142 " pdb=" C THR H 142 " ideal model delta sigma weight residual 113.20 107.62 5.58 1.21e+00 6.83e-01 2.13e+01 ... (remaining 19400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7543 17.94 - 35.87: 630 35.87 - 53.81: 115 53.81 - 71.75: 15 71.75 - 89.68: 12 Dihedral angle restraints: 8315 sinusoidal: 3239 harmonic: 5076 Sorted by residual: dihedral pdb=" CB CYS L 61 " pdb=" SG CYS L 61 " pdb=" SG CYS K 61 " pdb=" CB CYS K 61 " ideal model delta sinusoidal sigma weight residual -86.00 -154.42 68.42 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS C 61 " pdb=" CB CYS C 61 " ideal model delta sinusoidal sigma weight residual -86.00 -33.88 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS J 61 " pdb=" SG CYS J 61 " pdb=" SG CYS I 61 " pdb=" CB CYS I 61 " ideal model delta sinusoidal sigma weight residual -86.00 -136.65 50.65 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 8312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1326 0.026 - 0.052: 546 0.052 - 0.079: 214 0.079 - 0.105: 97 0.105 - 0.131: 28 Chirality restraints: 2211 Sorted by residual: chirality pdb=" CA ASP K 22 " pdb=" N ASP K 22 " pdb=" C ASP K 22 " pdb=" CB ASP K 22 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE L 3 " pdb=" N ILE L 3 " pdb=" C ILE L 3 " pdb=" CB ILE L 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA PRO I 135 " pdb=" N PRO I 135 " pdb=" C PRO I 135 " pdb=" CB PRO I 135 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2208 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 21 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C SER C 21 " -0.047 2.00e-02 2.50e+03 pdb=" O SER C 21 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 22 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 139 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ILE L 139 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE L 139 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU L 140 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 21 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C SER G 21 " -0.038 2.00e-02 2.50e+03 pdb=" O SER G 21 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP G 22 " 0.013 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 103 2.50 - 3.10: 11034 3.10 - 3.70: 21447 3.70 - 4.30: 27991 4.30 - 4.90: 46413 Nonbonded interactions: 106988 Sorted by model distance: nonbonded pdb=" NZ LYS H 96 " pdb=" OD2 ASP G 64 " model vdw 1.896 2.520 nonbonded pdb=" OD1 ASP F 78 " pdb=" OG SER F 81 " model vdw 1.919 2.440 nonbonded pdb=" O GLU L 14 " pdb=" OG SER L 17 " model vdw 2.106 2.440 nonbonded pdb=" O THR E 128 " pdb=" NH2 ARG E 133 " model vdw 2.114 2.520 nonbonded pdb=" O LEU A 76 " pdb=" NH2 ARG A 82 " model vdw 2.123 2.520 ... (remaining 106983 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' and resid 1 through 142) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 142) selection = chain 'G' selection = (chain 'H' and resid 1 through 142) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 1 through 142) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.150 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.720 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.050 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.004 0.052 14150 Z= 0.249 Angle : 0.700 10.279 19405 Z= 0.409 Chirality : 0.037 0.131 2211 Planarity : 0.005 0.056 2464 Dihedral : 13.672 89.685 4999 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 1.06 % Allowed : 0.26 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.21), residues: 1700 helix: 1.76 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -0.33 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 71 HIS 0.004 0.001 HIS L 47 PHE 0.027 0.001 PHE H 122 TYR 0.018 0.001 TYR H 118 ARG 0.010 0.001 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 524 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9112 (tt0) cc_final: 0.8689 (mt0) REVERT: A 12 THR cc_start: 0.8501 (p) cc_final: 0.8277 (p) REVERT: A 39 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8832 (ttm170) REVERT: A 83 ASP cc_start: 0.7174 (p0) cc_final: 0.6892 (m-30) REVERT: D 8 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 61 CYS cc_start: 0.7162 (m) cc_final: 0.6640 (m) REVERT: D 121 SER cc_start: 0.8879 (t) cc_final: 0.8624 (m) REVERT: C 7 LYS cc_start: 0.8934 (tttm) cc_final: 0.8494 (ttmm) REVERT: F 7 LYS cc_start: 0.9304 (tttp) cc_final: 0.9063 (tttp) REVERT: F 59 ILE cc_start: 0.7855 (tt) cc_final: 0.7466 (pt) REVERT: F 62 TRP cc_start: 0.8802 (t-100) cc_final: 0.8515 (t-100) REVERT: E 112 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7321 (ptp-170) REVERT: H 22 ASP cc_start: 0.6576 (t70) cc_final: 0.6220 (t70) REVERT: H 82 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7664 (mmm-85) REVERT: H 87 SER cc_start: 0.8988 (t) cc_final: 0.8441 (p) REVERT: H 125 TRP cc_start: 0.8840 (t60) cc_final: 0.8554 (t60) REVERT: G 48 CYS cc_start: 0.5637 (p) cc_final: 0.4529 (t) REVERT: G 142 THR cc_start: 0.8300 (m) cc_final: 0.7962 (p) REVERT: J 7 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8584 (ttmt) REVERT: J 88 TYR cc_start: 0.7761 (t80) cc_final: 0.7484 (t80) REVERT: J 136 ASN cc_start: 0.9092 (p0) cc_final: 0.8783 (p0) REVERT: I 7 LYS cc_start: 0.8878 (tppp) cc_final: 0.8626 (tptp) REVERT: I 18 PHE cc_start: 0.8878 (t80) cc_final: 0.8405 (t80) REVERT: I 39 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8008 (mtp85) REVERT: I 64 ASP cc_start: 0.8890 (m-30) cc_final: 0.8536 (m-30) REVERT: L 38 TYR cc_start: 0.8659 (m-80) cc_final: 0.8421 (m-10) REVERT: L 66 MET cc_start: 0.8228 (mmm) cc_final: 0.7357 (mmp) REVERT: L 96 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7933 (ttpt) REVERT: L 145 GLU cc_start: 0.6454 (tp30) cc_final: 0.6104 (tp30) REVERT: K 59 ILE cc_start: 0.8219 (mm) cc_final: 0.7860 (mm) outliers start: 16 outliers final: 5 residues processed: 527 average time/residue: 0.2585 time to fit residues: 193.2786 Evaluate side-chains 390 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 385 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 0.0010 chunk 153 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 104 HIS C 52 HIS ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 136 ASN J 52 HIS J 57 GLN L 52 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14150 Z= 0.220 Angle : 0.680 10.294 19405 Z= 0.339 Chirality : 0.042 0.243 2211 Planarity : 0.005 0.042 2464 Dihedral : 4.610 50.603 1876 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 2.90 % Allowed : 11.49 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1700 helix: 1.78 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : 0.02 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 71 HIS 0.012 0.001 HIS A 47 PHE 0.025 0.002 PHE C 18 TYR 0.028 0.002 TYR G 38 ARG 0.007 0.001 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 425 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9018 (tt0) cc_final: 0.8330 (tt0) REVERT: A 83 ASP cc_start: 0.6939 (p0) cc_final: 0.6690 (m-30) REVERT: D 8 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7794 (tm-30) REVERT: D 61 CYS cc_start: 0.7023 (m) cc_final: 0.6623 (m) REVERT: D 121 SER cc_start: 0.8958 (t) cc_final: 0.8705 (m) REVERT: C 7 LYS cc_start: 0.8941 (tttm) cc_final: 0.8426 (ttmm) REVERT: C 9 PHE cc_start: 0.8022 (m-80) cc_final: 0.7722 (m-10) REVERT: C 66 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7966 (mpp) REVERT: C 119 LEU cc_start: 0.8747 (tt) cc_final: 0.8466 (tt) REVERT: F 7 LYS cc_start: 0.9147 (tttp) cc_final: 0.8925 (tttp) REVERT: F 18 PHE cc_start: 0.7528 (m-10) cc_final: 0.7314 (m-10) REVERT: F 19 LEU cc_start: 0.9242 (mt) cc_final: 0.8998 (mt) REVERT: F 62 TRP cc_start: 0.8777 (t-100) cc_final: 0.7986 (t-100) REVERT: F 96 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7768 (tmmt) REVERT: E 117 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8173 (mm-30) REVERT: H 8 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6618 (tm-30) REVERT: H 22 ASP cc_start: 0.6694 (t70) cc_final: 0.6378 (t70) REVERT: H 82 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7501 (mmm-85) REVERT: H 125 TRP cc_start: 0.8983 (t60) cc_final: 0.8772 (t60) REVERT: G 40 ASP cc_start: 0.8198 (m-30) cc_final: 0.7865 (m-30) REVERT: G 78 ASP cc_start: 0.7373 (t0) cc_final: 0.6493 (t0) REVERT: J 8 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7859 (tm-30) REVERT: I 7 LYS cc_start: 0.8970 (tppp) cc_final: 0.8660 (tptp) REVERT: I 64 ASP cc_start: 0.8555 (m-30) cc_final: 0.8342 (m-30) REVERT: L 38 TYR cc_start: 0.8891 (m-80) cc_final: 0.8538 (m-10) REVERT: L 66 MET cc_start: 0.8288 (mmm) cc_final: 0.7783 (tpp) REVERT: K 59 ILE cc_start: 0.8190 (mm) cc_final: 0.7986 (mm) REVERT: K 66 MET cc_start: 0.7244 (mmp) cc_final: 0.6764 (mmt) REVERT: K 112 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7622 (ttm-80) outliers start: 44 outliers final: 29 residues processed: 441 average time/residue: 0.2625 time to fit residues: 165.8455 Evaluate side-chains 404 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 374 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 PHE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 128 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 153 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS G 136 ASN J 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14150 Z= 0.275 Angle : 0.672 10.365 19405 Z= 0.341 Chirality : 0.044 0.231 2211 Planarity : 0.005 0.070 2464 Dihedral : 4.366 42.792 1871 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 4.49 % Allowed : 15.97 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.21), residues: 1700 helix: 1.62 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : 0.14 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 102 HIS 0.007 0.002 HIS A 47 PHE 0.027 0.002 PHE C 18 TYR 0.021 0.002 TYR E 88 ARG 0.006 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 416 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.5998 (tpm170) REVERT: B 99 GLN cc_start: 0.9100 (tt0) cc_final: 0.8609 (tt0) REVERT: A 37 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9088 (tt) REVERT: A 38 TYR cc_start: 0.8880 (m-80) cc_final: 0.8564 (m-80) REVERT: A 83 ASP cc_start: 0.7332 (p0) cc_final: 0.6747 (m-30) REVERT: D 61 CYS cc_start: 0.6991 (m) cc_final: 0.6442 (m) REVERT: D 99 GLN cc_start: 0.8053 (tt0) cc_final: 0.7782 (pt0) REVERT: C 7 LYS cc_start: 0.8953 (tttm) cc_final: 0.8467 (ttmm) REVERT: C 39 ARG cc_start: 0.8208 (tpt-90) cc_final: 0.7825 (ttm-80) REVERT: F 57 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8235 (mm-40) REVERT: F 59 ILE cc_start: 0.8132 (pt) cc_final: 0.7854 (mt) REVERT: F 126 ILE cc_start: 0.9407 (tp) cc_final: 0.9169 (tp) REVERT: E 99 GLN cc_start: 0.8816 (mt0) cc_final: 0.8524 (mt0) REVERT: H 60 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8662 (mm) REVERT: H 82 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7438 (mmm-85) REVERT: H 99 GLN cc_start: 0.8478 (tt0) cc_final: 0.8227 (tt0) REVERT: G 14 GLU cc_start: 0.7930 (pt0) cc_final: 0.7623 (pt0) REVERT: G 78 ASP cc_start: 0.7589 (t0) cc_final: 0.6485 (t0) REVERT: G 121 SER cc_start: 0.8813 (t) cc_final: 0.8251 (p) REVERT: J 8 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8109 (tm-30) REVERT: J 82 ARG cc_start: 0.6211 (mtm180) cc_final: 0.5851 (mtt180) REVERT: I 14 GLU cc_start: 0.7258 (pp20) cc_final: 0.7029 (pp20) REVERT: I 74 THR cc_start: 0.8558 (m) cc_final: 0.8218 (p) REVERT: I 117 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8263 (mm-30) REVERT: L 66 MET cc_start: 0.8442 (mmm) cc_final: 0.7766 (tpp) REVERT: L 90 ASN cc_start: 0.8599 (t0) cc_final: 0.8235 (m-40) REVERT: L 117 GLU cc_start: 0.7314 (tp30) cc_final: 0.6858 (tp30) REVERT: L 145 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6458 (mm-30) REVERT: K 117 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7704 (mp0) outliers start: 68 outliers final: 46 residues processed: 448 average time/residue: 0.2437 time to fit residues: 156.7743 Evaluate side-chains 429 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 380 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN J 92 ASN L 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14150 Z= 0.225 Angle : 0.631 11.412 19405 Z= 0.315 Chirality : 0.042 0.241 2211 Planarity : 0.004 0.044 2464 Dihedral : 4.228 43.284 1871 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 3.89 % Allowed : 19.60 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1700 helix: 1.73 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : 0.15 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 71 HIS 0.006 0.001 HIS A 47 PHE 0.016 0.001 PHE C 18 TYR 0.013 0.001 TYR B 118 ARG 0.006 0.000 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 403 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9182 (tt0) cc_final: 0.8606 (tt0) REVERT: A 37 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9188 (tt) REVERT: A 83 ASP cc_start: 0.7311 (p0) cc_final: 0.6716 (m-30) REVERT: D 99 GLN cc_start: 0.8174 (tt0) cc_final: 0.7941 (pt0) REVERT: C 7 LYS cc_start: 0.8835 (tttm) cc_final: 0.8434 (ttmm) REVERT: C 39 ARG cc_start: 0.8279 (tpt-90) cc_final: 0.7763 (ttm-80) REVERT: F 59 ILE cc_start: 0.8114 (pt) cc_final: 0.7871 (mt) REVERT: F 126 ILE cc_start: 0.9491 (tp) cc_final: 0.9260 (tp) REVERT: E 3 ILE cc_start: 0.9462 (mm) cc_final: 0.8287 (tt) REVERT: E 99 GLN cc_start: 0.8855 (mt0) cc_final: 0.8568 (mt0) REVERT: H 70 THR cc_start: 0.8848 (m) cc_final: 0.8309 (p) REVERT: H 99 GLN cc_start: 0.8474 (tt0) cc_final: 0.8263 (tt0) REVERT: H 117 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8132 (mm-30) REVERT: G 14 GLU cc_start: 0.8025 (pt0) cc_final: 0.7703 (pt0) REVERT: G 78 ASP cc_start: 0.7723 (t0) cc_final: 0.6943 (t0) REVERT: G 82 ARG cc_start: 0.7863 (ptp90) cc_final: 0.7551 (ptt-90) REVERT: G 121 SER cc_start: 0.8812 (t) cc_final: 0.8267 (p) REVERT: J 8 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8318 (tm-30) REVERT: J 40 ASP cc_start: 0.8381 (p0) cc_final: 0.8122 (p0) REVERT: J 66 MET cc_start: 0.8636 (mmp) cc_final: 0.8410 (mmm) REVERT: I 57 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: I 117 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8186 (mm-30) REVERT: L 117 GLU cc_start: 0.7182 (tp30) cc_final: 0.6763 (tp30) REVERT: K 70 THR cc_start: 0.8300 (m) cc_final: 0.8050 (p) REVERT: K 86 VAL cc_start: 0.8573 (t) cc_final: 0.8360 (p) REVERT: K 88 TYR cc_start: 0.9118 (t80) cc_final: 0.8750 (t80) REVERT: K 96 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7558 (ptpt) REVERT: K 108 LEU cc_start: 0.8841 (tt) cc_final: 0.8526 (tp) REVERT: K 117 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7886 (mp0) outliers start: 59 outliers final: 41 residues processed: 424 average time/residue: 0.2394 time to fit residues: 146.0975 Evaluate side-chains 428 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 383 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 141 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 139 optimal weight: 0.0270 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.0980 chunk 146 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14150 Z= 0.212 Angle : 0.620 10.441 19405 Z= 0.309 Chirality : 0.041 0.240 2211 Planarity : 0.005 0.070 2464 Dihedral : 4.117 44.139 1870 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 4.16 % Allowed : 20.79 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.21), residues: 1700 helix: 1.76 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : 0.16 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 71 HIS 0.027 0.001 HIS A 47 PHE 0.017 0.001 PHE K 110 TYR 0.020 0.001 TYR L 38 ARG 0.006 0.000 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 413 time to evaluate : 2.878 Fit side-chains revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9187 (tt0) cc_final: 0.8675 (tt0) REVERT: B 117 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7546 (mm-30) REVERT: A 37 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9171 (tt) REVERT: A 62 TRP cc_start: 0.8126 (t-100) cc_final: 0.7429 (t-100) REVERT: A 83 ASP cc_start: 0.7305 (p0) cc_final: 0.6718 (m-30) REVERT: D 26 SER cc_start: 0.8495 (t) cc_final: 0.7736 (p) REVERT: D 99 GLN cc_start: 0.8149 (tt0) cc_final: 0.7937 (pt0) REVERT: C 7 LYS cc_start: 0.8803 (tttm) cc_final: 0.8404 (ttmm) REVERT: C 39 ARG cc_start: 0.8270 (tpt-90) cc_final: 0.7750 (ttm-80) REVERT: C 55 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 119 LEU cc_start: 0.8946 (tt) cc_final: 0.8718 (tt) REVERT: F 59 ILE cc_start: 0.8176 (pt) cc_final: 0.7924 (mt) REVERT: F 117 GLU cc_start: 0.4668 (tm-30) cc_final: 0.4320 (tm-30) REVERT: F 126 ILE cc_start: 0.9511 (tp) cc_final: 0.9290 (tp) REVERT: E 3 ILE cc_start: 0.9448 (mm) cc_final: 0.8328 (tt) REVERT: E 99 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: H 70 THR cc_start: 0.8775 (m) cc_final: 0.8262 (p) REVERT: H 88 TYR cc_start: 0.8267 (t80) cc_final: 0.8000 (t80) REVERT: H 99 GLN cc_start: 0.8618 (tt0) cc_final: 0.8416 (tt0) REVERT: H 117 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8152 (mm-30) REVERT: G 14 GLU cc_start: 0.8003 (pt0) cc_final: 0.7721 (pt0) REVERT: G 78 ASP cc_start: 0.7823 (t0) cc_final: 0.7013 (t0) REVERT: G 82 ARG cc_start: 0.7984 (ptp90) cc_final: 0.7778 (ptp90) REVERT: G 121 SER cc_start: 0.8809 (t) cc_final: 0.8263 (p) REVERT: J 8 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8310 (tm-30) REVERT: J 40 ASP cc_start: 0.8387 (p0) cc_final: 0.8065 (p0) REVERT: J 66 MET cc_start: 0.8670 (mmp) cc_final: 0.8449 (mmm) REVERT: I 57 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7913 (mp10) REVERT: I 117 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8165 (mm-30) REVERT: L 82 ARG cc_start: 0.6651 (ptp90) cc_final: 0.6269 (ptm160) REVERT: L 88 TYR cc_start: 0.8591 (t80) cc_final: 0.8356 (t80) REVERT: L 90 ASN cc_start: 0.8710 (t0) cc_final: 0.8494 (m-40) REVERT: L 117 GLU cc_start: 0.7181 (tp30) cc_final: 0.6761 (tp30) REVERT: K 66 MET cc_start: 0.7361 (mmp) cc_final: 0.7053 (mmp) REVERT: K 86 VAL cc_start: 0.8664 (t) cc_final: 0.8424 (p) REVERT: K 88 TYR cc_start: 0.9070 (t80) cc_final: 0.8825 (t80) REVERT: K 96 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7553 (ptpt) REVERT: K 108 LEU cc_start: 0.8811 (tt) cc_final: 0.8516 (tp) REVERT: K 117 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8016 (mp0) outliers start: 63 outliers final: 47 residues processed: 437 average time/residue: 0.2549 time to fit residues: 160.0859 Evaluate side-chains 452 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 399 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.0010 chunk 85 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14150 Z= 0.357 Angle : 0.707 11.490 19405 Z= 0.359 Chirality : 0.045 0.223 2211 Planarity : 0.005 0.053 2464 Dihedral : 4.411 50.540 1870 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 6.20 % Allowed : 21.06 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.21), residues: 1700 helix: 1.50 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : 0.06 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 102 HIS 0.008 0.002 HIS K 104 PHE 0.027 0.002 PHE C 18 TYR 0.023 0.002 TYR L 38 ARG 0.010 0.001 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 430 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 28 ARG cc_start: 0.7442 (tpp-160) cc_final: 0.7160 (tpp-160) REVERT: B 31 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8700 (mt) REVERT: B 38 TYR cc_start: 0.8818 (m-10) cc_final: 0.8514 (m-10) REVERT: B 96 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8418 (ttmm) REVERT: B 99 GLN cc_start: 0.9181 (tt0) cc_final: 0.8664 (tt0) REVERT: A 37 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9211 (tt) REVERT: A 38 TYR cc_start: 0.8789 (m-80) cc_final: 0.8538 (m-80) REVERT: A 62 TRP cc_start: 0.8354 (t-100) cc_final: 0.7602 (t-100) REVERT: A 83 ASP cc_start: 0.7406 (p0) cc_final: 0.6740 (m-30) REVERT: D 61 CYS cc_start: 0.7190 (m) cc_final: 0.6826 (m) REVERT: C 7 LYS cc_start: 0.8833 (tttm) cc_final: 0.8471 (ttmm) REVERT: C 55 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7973 (tt) REVERT: C 75 ASN cc_start: 0.6787 (m-40) cc_final: 0.6444 (t0) REVERT: F 28 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7847 (mmm160) REVERT: F 29 ASP cc_start: 0.9000 (m-30) cc_final: 0.8681 (m-30) REVERT: F 67 THR cc_start: 0.8557 (m) cc_final: 0.8227 (t) REVERT: F 126 ILE cc_start: 0.9433 (tp) cc_final: 0.9233 (tp) REVERT: E 3 ILE cc_start: 0.9606 (mm) cc_final: 0.8547 (tt) REVERT: E 95 LEU cc_start: 0.8829 (tt) cc_final: 0.8601 (tp) REVERT: E 99 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8658 (mt0) REVERT: H 70 THR cc_start: 0.8900 (m) cc_final: 0.8354 (p) REVERT: H 99 GLN cc_start: 0.8841 (tt0) cc_final: 0.8633 (tt0) REVERT: G 78 ASP cc_start: 0.8084 (t0) cc_final: 0.7452 (t0) REVERT: G 121 SER cc_start: 0.8957 (t) cc_final: 0.8657 (t) REVERT: J 66 MET cc_start: 0.8757 (mmp) cc_final: 0.8335 (mmm) REVERT: J 141 SER cc_start: 0.9644 (m) cc_final: 0.9099 (p) REVERT: I 57 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: I 136 ASN cc_start: 0.8796 (p0) cc_final: 0.8470 (p0) REVERT: L 8 GLU cc_start: 0.6956 (pp20) cc_final: 0.6597 (pp20) REVERT: L 66 MET cc_start: 0.8545 (tpp) cc_final: 0.8048 (mpp) REVERT: L 117 GLU cc_start: 0.7471 (tp30) cc_final: 0.7053 (tp30) REVERT: K 32 ASP cc_start: 0.7872 (t0) cc_final: 0.7621 (t0) REVERT: K 66 MET cc_start: 0.7936 (mmp) cc_final: 0.7631 (mmp) REVERT: K 86 VAL cc_start: 0.8753 (t) cc_final: 0.8508 (p) REVERT: K 108 LEU cc_start: 0.8931 (tt) cc_final: 0.8658 (tp) outliers start: 94 outliers final: 71 residues processed: 478 average time/residue: 0.2577 time to fit residues: 177.2461 Evaluate side-chains 485 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 409 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14150 Z= 0.265 Angle : 0.672 11.520 19405 Z= 0.337 Chirality : 0.043 0.214 2211 Planarity : 0.005 0.074 2464 Dihedral : 4.303 51.598 1870 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 5.35 % Allowed : 23.23 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1700 helix: 1.57 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 71 HIS 0.013 0.001 HIS A 47 PHE 0.029 0.002 PHE K 110 TYR 0.024 0.002 TYR L 38 ARG 0.009 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 425 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 28 ARG cc_start: 0.7588 (tpp-160) cc_final: 0.7362 (tpp-160) REVERT: B 31 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8671 (mt) REVERT: B 38 TYR cc_start: 0.8742 (m-10) cc_final: 0.8396 (m-10) REVERT: B 99 GLN cc_start: 0.9118 (tt0) cc_final: 0.8651 (tt0) REVERT: A 18 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8239 (m-10) REVERT: A 23 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6983 (p90) REVERT: A 37 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9204 (tt) REVERT: A 38 TYR cc_start: 0.8753 (m-80) cc_final: 0.8498 (m-80) REVERT: A 62 TRP cc_start: 0.8266 (t-100) cc_final: 0.7568 (t-100) REVERT: A 77 GLU cc_start: 0.7337 (mp0) cc_final: 0.7112 (mp0) REVERT: A 83 ASP cc_start: 0.7388 (p0) cc_final: 0.6738 (m-30) REVERT: A 88 TYR cc_start: 0.7930 (t80) cc_final: 0.7684 (t80) REVERT: A 95 LEU cc_start: 0.8396 (tt) cc_final: 0.8173 (tp) REVERT: C 7 LYS cc_start: 0.8763 (tttm) cc_final: 0.8379 (ttmm) REVERT: C 55 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7922 (tt) REVERT: C 75 ASN cc_start: 0.6830 (m-40) cc_final: 0.6481 (t0) REVERT: F 29 ASP cc_start: 0.8971 (m-30) cc_final: 0.8735 (m-30) REVERT: F 96 LYS cc_start: 0.9067 (tmmt) cc_final: 0.7944 (ttmt) REVERT: E 3 ILE cc_start: 0.9614 (mm) cc_final: 0.8585 (tt) REVERT: E 28 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7794 (tpp-160) REVERT: E 99 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: H 64 ASP cc_start: 0.8835 (m-30) cc_final: 0.8587 (m-30) REVERT: H 70 THR cc_start: 0.8831 (m) cc_final: 0.8374 (p) REVERT: H 99 GLN cc_start: 0.8847 (tt0) cc_final: 0.8617 (tt0) REVERT: H 121 SER cc_start: 0.9391 (m) cc_final: 0.9166 (t) REVERT: G 39 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7325 (ttm170) REVERT: G 78 ASP cc_start: 0.8224 (t0) cc_final: 0.7520 (t0) REVERT: G 112 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8152 (ttm110) REVERT: G 121 SER cc_start: 0.8937 (t) cc_final: 0.8648 (t) REVERT: J 40 ASP cc_start: 0.8491 (p0) cc_final: 0.8108 (p0) REVERT: J 66 MET cc_start: 0.8775 (mmp) cc_final: 0.8372 (mmm) REVERT: J 141 SER cc_start: 0.9659 (m) cc_final: 0.9125 (p) REVERT: I 57 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: I 119 LEU cc_start: 0.9177 (mt) cc_final: 0.8259 (mt) REVERT: I 136 ASN cc_start: 0.8802 (p0) cc_final: 0.8499 (p0) REVERT: L 88 TYR cc_start: 0.8820 (t80) cc_final: 0.8479 (t80) REVERT: L 117 GLU cc_start: 0.7326 (tp30) cc_final: 0.6941 (tp30) REVERT: K 66 MET cc_start: 0.7936 (mmp) cc_final: 0.7655 (mmp) REVERT: K 86 VAL cc_start: 0.8796 (t) cc_final: 0.8507 (p) REVERT: K 108 LEU cc_start: 0.8863 (tt) cc_final: 0.8564 (tp) REVERT: K 117 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7116 (mp0) outliers start: 81 outliers final: 57 residues processed: 463 average time/residue: 0.2617 time to fit residues: 175.5263 Evaluate side-chains 484 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 418 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 4 ASP Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14150 Z= 0.213 Angle : 0.662 11.267 19405 Z= 0.327 Chirality : 0.042 0.231 2211 Planarity : 0.005 0.065 2464 Dihedral : 4.198 54.470 1870 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 4.62 % Allowed : 23.96 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1700 helix: 1.66 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.14 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 102 HIS 0.005 0.001 HIS L 51 PHE 0.037 0.001 PHE K 110 TYR 0.024 0.002 TYR L 38 ARG 0.009 0.001 ARG G 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 430 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8709 (mt) REVERT: B 38 TYR cc_start: 0.8684 (m-10) cc_final: 0.8404 (m-10) REVERT: B 68 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7285 (tt) REVERT: B 99 GLN cc_start: 0.9116 (tt0) cc_final: 0.8664 (tt0) REVERT: A 18 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8244 (m-10) REVERT: A 37 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9191 (tt) REVERT: A 38 TYR cc_start: 0.8749 (m-80) cc_final: 0.8538 (m-80) REVERT: A 62 TRP cc_start: 0.8195 (t-100) cc_final: 0.7422 (t-100) REVERT: A 83 ASP cc_start: 0.7352 (p0) cc_final: 0.6718 (m-30) REVERT: A 95 LEU cc_start: 0.8196 (tt) cc_final: 0.7970 (tp) REVERT: D 60 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9172 (mm) REVERT: D 99 GLN cc_start: 0.7781 (tt0) cc_final: 0.7455 (tt0) REVERT: C 7 LYS cc_start: 0.8700 (tttm) cc_final: 0.8360 (ttmm) REVERT: C 21 SER cc_start: 0.8802 (m) cc_final: 0.8112 (p) REVERT: C 55 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7806 (tt) REVERT: C 75 ASN cc_start: 0.6750 (m-40) cc_final: 0.6198 (m110) REVERT: F 29 ASP cc_start: 0.8968 (m-30) cc_final: 0.8731 (m-30) REVERT: F 96 LYS cc_start: 0.9023 (tmmt) cc_final: 0.7906 (ttmt) REVERT: F 117 GLU cc_start: 0.5336 (tm-30) cc_final: 0.5132 (tm-30) REVERT: E 3 ILE cc_start: 0.9712 (mm) cc_final: 0.8585 (tt) REVERT: E 28 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7785 (tpp-160) REVERT: E 99 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: E 127 ARG cc_start: 0.8956 (mmt-90) cc_final: 0.8751 (mmt-90) REVERT: H 70 THR cc_start: 0.8703 (m) cc_final: 0.8467 (t) REVERT: H 77 GLU cc_start: 0.7102 (mp0) cc_final: 0.6715 (mp0) REVERT: H 99 GLN cc_start: 0.8804 (tt0) cc_final: 0.8574 (tt0) REVERT: H 121 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9130 (t) REVERT: G 39 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7196 (ttm170) REVERT: G 121 SER cc_start: 0.8859 (t) cc_final: 0.8619 (t) REVERT: J 6 TYR cc_start: 0.8045 (m-10) cc_final: 0.7811 (m-10) REVERT: J 40 ASP cc_start: 0.8493 (p0) cc_final: 0.8045 (p0) REVERT: J 66 MET cc_start: 0.8755 (mmp) cc_final: 0.8371 (mmm) REVERT: J 141 SER cc_start: 0.9667 (m) cc_final: 0.9157 (p) REVERT: I 57 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: I 107 CYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8306 (t) REVERT: I 119 LEU cc_start: 0.8952 (mt) cc_final: 0.7872 (mt) REVERT: I 136 ASN cc_start: 0.8420 (p0) cc_final: 0.8130 (p0) REVERT: L 8 GLU cc_start: 0.8536 (pm20) cc_final: 0.7835 (pp20) REVERT: L 117 GLU cc_start: 0.7228 (tp30) cc_final: 0.6884 (tp30) REVERT: K 16 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8762 (mt) REVERT: K 66 MET cc_start: 0.7894 (mmp) cc_final: 0.7157 (tpp) REVERT: K 86 VAL cc_start: 0.8879 (t) cc_final: 0.8608 (p) REVERT: K 108 LEU cc_start: 0.8834 (tt) cc_final: 0.8551 (tp) REVERT: K 117 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7098 (mp0) outliers start: 70 outliers final: 46 residues processed: 461 average time/residue: 0.2652 time to fit residues: 176.1612 Evaluate side-chains 470 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 411 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 4 ASP Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN J 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14150 Z= 0.261 Angle : 0.678 11.106 19405 Z= 0.338 Chirality : 0.044 0.228 2211 Planarity : 0.005 0.061 2464 Dihedral : 4.218 57.556 1870 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 4.82 % Allowed : 24.36 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1700 helix: 1.63 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : 0.12 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 62 HIS 0.005 0.001 HIS L 104 PHE 0.034 0.002 PHE K 110 TYR 0.025 0.002 TYR L 38 ARG 0.009 0.001 ARG L 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 421 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8292 (mp) REVERT: B 38 TYR cc_start: 0.8757 (m-10) cc_final: 0.8461 (m-10) REVERT: B 99 GLN cc_start: 0.9131 (tt0) cc_final: 0.8687 (tt0) REVERT: A 18 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: A 37 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9154 (tt) REVERT: A 38 TYR cc_start: 0.8777 (m-80) cc_final: 0.8572 (m-80) REVERT: A 62 TRP cc_start: 0.8264 (t-100) cc_final: 0.7475 (t-100) REVERT: A 83 ASP cc_start: 0.7392 (p0) cc_final: 0.6707 (m-30) REVERT: A 95 LEU cc_start: 0.8224 (tt) cc_final: 0.8001 (tp) REVERT: C 7 LYS cc_start: 0.8738 (tttm) cc_final: 0.8406 (ttmm) REVERT: C 21 SER cc_start: 0.8872 (m) cc_final: 0.8074 (p) REVERT: C 55 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7839 (tt) REVERT: C 75 ASN cc_start: 0.6786 (m-40) cc_final: 0.6253 (m110) REVERT: F 28 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7787 (mmm160) REVERT: F 29 ASP cc_start: 0.9027 (m-30) cc_final: 0.8717 (m-30) REVERT: F 62 TRP cc_start: 0.8871 (t-100) cc_final: 0.8574 (t-100) REVERT: F 96 LYS cc_start: 0.8843 (tmmt) cc_final: 0.8027 (ttmt) REVERT: E 3 ILE cc_start: 0.9691 (mm) cc_final: 0.8646 (tt) REVERT: E 28 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7996 (tpp-160) REVERT: E 99 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8593 (mt0) REVERT: H 77 GLU cc_start: 0.7050 (mp0) cc_final: 0.6735 (mp0) REVERT: H 99 GLN cc_start: 0.8831 (tt0) cc_final: 0.8567 (tt0) REVERT: G 121 SER cc_start: 0.8936 (t) cc_final: 0.8621 (t) REVERT: J 66 MET cc_start: 0.8761 (mmp) cc_final: 0.8411 (mmm) REVERT: J 141 SER cc_start: 0.9654 (m) cc_final: 0.9190 (p) REVERT: I 57 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: I 119 LEU cc_start: 0.9136 (mt) cc_final: 0.8239 (mt) REVERT: I 136 ASN cc_start: 0.8823 (p0) cc_final: 0.8526 (p0) REVERT: L 8 GLU cc_start: 0.8593 (pm20) cc_final: 0.7764 (pp20) REVERT: L 117 GLU cc_start: 0.7381 (tp30) cc_final: 0.6913 (tp30) REVERT: K 86 VAL cc_start: 0.8910 (t) cc_final: 0.8648 (p) REVERT: K 108 LEU cc_start: 0.8873 (tt) cc_final: 0.8625 (tp) REVERT: K 117 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7104 (mp0) outliers start: 73 outliers final: 54 residues processed: 455 average time/residue: 0.2627 time to fit residues: 172.7420 Evaluate side-chains 468 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 406 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 8 GLU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 0.0040 chunk 168 optimal weight: 0.3980 chunk 154 optimal weight: 0.8980 chunk 134 optimal weight: 0.0050 chunk 13 optimal weight: 0.0050 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.2420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14150 Z= 0.187 Angle : 0.675 13.567 19405 Z= 0.329 Chirality : 0.042 0.253 2211 Planarity : 0.005 0.057 2464 Dihedral : 3.984 50.706 1870 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.98 % Allowed : 27.85 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.21), residues: 1700 helix: 1.71 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : 0.32 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 62 HIS 0.004 0.001 HIS L 51 PHE 0.028 0.001 PHE K 18 TYR 0.026 0.002 TYR E 88 ARG 0.009 0.001 ARG G 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 442 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7401 (tt) REVERT: B 99 GLN cc_start: 0.9183 (tt0) cc_final: 0.8780 (mt0) REVERT: A 37 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9195 (tt) REVERT: A 38 TYR cc_start: 0.8747 (m-80) cc_final: 0.8504 (m-80) REVERT: A 62 TRP cc_start: 0.8076 (t-100) cc_final: 0.7366 (t-100) REVERT: A 83 ASP cc_start: 0.7318 (p0) cc_final: 0.6663 (m-30) REVERT: A 95 LEU cc_start: 0.8046 (tt) cc_final: 0.7830 (tp) REVERT: C 21 SER cc_start: 0.8306 (m) cc_final: 0.7631 (p) REVERT: C 55 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7831 (tt) REVERT: C 75 ASN cc_start: 0.6636 (m-40) cc_final: 0.6382 (t0) REVERT: F 29 ASP cc_start: 0.8974 (m-30) cc_final: 0.8754 (m-30) REVERT: F 96 LYS cc_start: 0.8913 (tmmt) cc_final: 0.7871 (ttmt) REVERT: E 3 ILE cc_start: 0.9688 (mm) cc_final: 0.8602 (tt) REVERT: E 28 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7775 (tpp-160) REVERT: E 43 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7877 (mm-30) REVERT: E 99 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8541 (mt0) REVERT: E 124 VAL cc_start: 0.9198 (t) cc_final: 0.8513 (p) REVERT: H 77 GLU cc_start: 0.6971 (mp0) cc_final: 0.6723 (mp0) REVERT: G 121 SER cc_start: 0.8869 (t) cc_final: 0.8604 (t) REVERT: J 66 MET cc_start: 0.8703 (mmp) cc_final: 0.8393 (mmm) REVERT: J 141 SER cc_start: 0.9647 (m) cc_final: 0.9159 (p) REVERT: I 30 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8327 (mm) REVERT: I 57 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: I 119 LEU cc_start: 0.8781 (mt) cc_final: 0.7814 (mt) REVERT: I 136 ASN cc_start: 0.8334 (p0) cc_final: 0.8024 (p0) REVERT: L 39 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7430 (tpp80) REVERT: L 117 GLU cc_start: 0.7163 (tp30) cc_final: 0.6714 (tp30) REVERT: K 16 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8703 (mt) REVERT: K 86 VAL cc_start: 0.8968 (t) cc_final: 0.8724 (p) REVERT: K 117 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7155 (mp0) outliers start: 30 outliers final: 22 residues processed: 455 average time/residue: 0.2486 time to fit residues: 162.7901 Evaluate side-chains 448 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 418 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.094554 restraints weight = 23511.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.096236 restraints weight = 17237.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.097553 restraints weight = 13910.446| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14150 Z= 0.305 Angle : 0.711 12.226 19405 Z= 0.354 Chirality : 0.045 0.218 2211 Planarity : 0.005 0.054 2464 Dihedral : 4.051 41.940 1870 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.29 % Rotamer: Outliers : 2.97 % Allowed : 28.45 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1700 helix: 1.69 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.01 (0.31), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 71 HIS 0.006 0.002 HIS K 104 PHE 0.055 0.002 PHE K 110 TYR 0.033 0.002 TYR K 118 ARG 0.010 0.001 ARG L 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.45 seconds wall clock time: 58 minutes 46.11 seconds (3526.11 seconds total)