Starting phenix.real_space_refine on Sat Feb 17 03:37:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/02_2024/8hxc_35076.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/02_2024/8hxc_35076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/02_2024/8hxc_35076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/02_2024/8hxc_35076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/02_2024/8hxc_35076.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hxc_35076/02_2024/8hxc_35076.pdb" } resolution = 3.12 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= 0.001 sd= 0.037 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 140 5.16 5 C 10941 2.51 5 N 2933 2.21 5 O 3360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17374 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "B" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "C" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "D" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "F" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "G" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain: "H" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "J" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "K" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "M" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "N" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 872 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Time building chain proxies: 8.80, per 1000 atoms: 0.51 Number of scatterers: 17374 At special positions: 0 Unit cell: (185.25, 183.35, 67.45, 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 140 16.00 O 3360 8.00 N 2933 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS G 25 " distance=2.04 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS C 130 " distance=1.99 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS D 130 " distance=2.05 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 217 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS E 130 " distance=2.07 Simple disulfide: pdb=" SG CYS D 56 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS F 130 " distance=2.01 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS G 130 " distance=2.02 Simple disulfide: pdb=" SG CYS F 56 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 160 " - pdb=" SG CYS F 205 " distance=2.02 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 217 " distance=2.03 Simple disulfide: pdb=" SG CYS G 125 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 160 " - pdb=" SG CYS G 205 " distance=2.02 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 110 " distance=2.03 Simple disulfide: pdb=" SG CYS I 40 " - pdb=" SG CYS I 110 " distance=2.03 Simple disulfide: pdb=" SG CYS J 40 " - pdb=" SG CYS J 110 " distance=2.03 Simple disulfide: pdb=" SG CYS K 40 " - pdb=" SG CYS K 110 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 110 " distance=2.03 Simple disulfide: pdb=" SG CYS M 40 " - pdb=" SG CYS M 110 " distance=2.03 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.96 Conformation dependent library (CDL) restraints added in 3.2 seconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 4.9% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.648A pdb=" N MET B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.649A pdb=" N MET E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.647A pdb=" N MET F 190 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.648A pdb=" N MET G 190 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU H 52 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 53' Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU I 52 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 53' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 49 through 53 removed outlier: 3.711A pdb=" N GLU J 52 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 53 " --> pdb=" O LEU J 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 49 through 53' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU K 52 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 49 through 53' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU L 52 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 53 " --> pdb=" O LEU L 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 49 through 53' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU M 52 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU M 53 " --> pdb=" O LEU M 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 49 through 53' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 49 through 53 removed outlier: 3.710A pdb=" N GLU N 52 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU N 53 " --> pdb=" O LEU N 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 49 through 53' Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE A 36 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR A 108 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 38 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS A 101 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 96 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 103 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 94 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 105 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 92 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 107 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 165 removed outlier: 9.443A pdb=" N SER A 193 " --> pdb=" O HIS H 124 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS H 124 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY A 195 " --> pdb=" O ARG H 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE H 112 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN H 125 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS H 110 " --> pdb=" O GLN H 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN H 127 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR H 108 " --> pdb=" O ASN H 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL H 55 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU H 67 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP H 57 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE B 36 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR B 108 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 38 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 101 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL B 96 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER B 103 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 94 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 105 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 92 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE B 107 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 165 removed outlier: 9.397A pdb=" N SER B 193 " --> pdb=" O HIS I 124 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS I 124 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY B 195 " --> pdb=" O ARG I 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE I 112 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN I 125 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS I 110 " --> pdb=" O GLN I 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN I 127 " --> pdb=" O TYR I 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR I 108 " --> pdb=" O ASN I 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL I 55 " --> pdb=" O GLU I 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU I 67 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP I 57 " --> pdb=" O LEU I 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE C 36 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR C 108 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA C 38 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS C 101 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL C 96 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER C 103 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 94 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 105 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA C 92 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE C 107 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 62 Processing sheet with id=AA9, first strand: chain 'C' and resid 160 through 165 removed outlier: 9.444A pdb=" N SER C 193 " --> pdb=" O HIS J 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS J 124 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY C 195 " --> pdb=" O ARG J 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE J 112 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN J 125 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS J 110 " --> pdb=" O GLN J 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN J 127 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR J 108 " --> pdb=" O ASN J 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 55 " --> pdb=" O GLU J 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU J 67 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP J 57 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 181 through 184 removed outlier: 5.530A pdb=" N PHE D 36 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR D 108 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 38 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS D 101 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL D 96 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER D 103 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU D 94 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU D 105 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 92 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE D 107 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 57 through 62 Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 165 removed outlier: 9.240A pdb=" N SER D 193 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS K 124 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLY D 195 " --> pdb=" O ARG K 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE K 112 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN K 125 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS K 110 " --> pdb=" O GLN K 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN K 127 " --> pdb=" O TYR K 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR K 108 " --> pdb=" O ASN K 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL K 55 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU K 67 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP K 57 " --> pdb=" O LEU K 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE E 36 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR E 108 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA E 38 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS E 101 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL E 96 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER E 103 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 94 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU E 105 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA E 92 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE E 107 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 62 Processing sheet with id=AB6, first strand: chain 'E' and resid 160 through 165 removed outlier: 9.501A pdb=" N SER E 193 " --> pdb=" O HIS L 124 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N HIS L 124 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY E 195 " --> pdb=" O ARG L 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE L 112 " --> pdb=" O ILE L 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN L 125 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS L 110 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN L 127 " --> pdb=" O TYR L 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR L 108 " --> pdb=" O ASN L 127 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL L 55 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU L 67 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 57 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE F 36 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR F 108 " --> pdb=" O PHE F 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 38 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS F 101 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 96 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER F 103 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU F 94 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU F 105 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA F 92 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 107 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 57 through 62 Processing sheet with id=AB9, first strand: chain 'F' and resid 160 through 165 removed outlier: 9.487A pdb=" N SER F 193 " --> pdb=" O HIS M 124 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS M 124 " --> pdb=" O SER F 193 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLY F 195 " --> pdb=" O ARG M 122 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE M 112 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN M 125 " --> pdb=" O CYS M 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS M 110 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN M 127 " --> pdb=" O TYR M 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR M 108 " --> pdb=" O ASN M 127 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL M 55 " --> pdb=" O GLU M 67 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU M 67 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP M 57 " --> pdb=" O LEU M 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 181 through 184 removed outlier: 5.531A pdb=" N PHE G 36 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 108 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 38 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 101 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL G 96 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER G 103 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU G 94 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 105 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA G 92 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE G 107 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 57 through 62 Processing sheet with id=AC3, first strand: chain 'G' and resid 160 through 165 removed outlier: 9.503A pdb=" N SER G 193 " --> pdb=" O HIS N 124 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N HIS N 124 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY G 195 " --> pdb=" O ARG N 122 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE N 112 " --> pdb=" O ILE N 123 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN N 125 " --> pdb=" O CYS N 110 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS N 110 " --> pdb=" O GLN N 125 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASN N 127 " --> pdb=" O TYR N 108 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR N 108 " --> pdb=" O ASN N 127 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL N 55 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU N 67 " --> pdb=" O VAL N 55 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP N 57 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 35 through 39 Processing sheet with id=AC5, first strand: chain 'I' and resid 35 through 39 Processing sheet with id=AC6, first strand: chain 'J' and resid 35 through 39 Processing sheet with id=AC7, first strand: chain 'K' and resid 35 through 39 Processing sheet with id=AC8, first strand: chain 'L' and resid 35 through 39 Processing sheet with id=AC9, first strand: chain 'M' and resid 35 through 39 Processing sheet with id=AD1, first strand: chain 'N' and resid 35 through 39 504 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5545 1.34 - 1.46: 4049 1.46 - 1.58: 7934 1.58 - 1.70: 7 1.70 - 1.83: 203 Bond restraints: 17738 Sorted by residual: bond pdb=" CA GLU L 52 " pdb=" CB GLU L 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.73e+01 bond pdb=" CA GLU M 52 " pdb=" CB GLU M 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.72e+01 bond pdb=" CA GLU J 52 " pdb=" CB GLU J 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.72e+01 bond pdb=" CA GLU H 52 " pdb=" CB GLU H 52 " ideal model delta sigma weight residual 1.527 1.630 -0.103 2.48e-02 1.63e+03 1.71e+01 bond pdb=" CA GLU N 52 " pdb=" CB GLU N 52 " ideal model delta sigma weight residual 1.527 1.630 -0.102 2.48e-02 1.63e+03 1.70e+01 ... (remaining 17733 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.12: 553 107.12 - 113.89: 9675 113.89 - 120.66: 6786 120.66 - 127.42: 6779 127.42 - 134.19: 217 Bond angle restraints: 24010 Sorted by residual: angle pdb=" C ASN F 203 " pdb=" N GLN F 204 " pdb=" CA GLN F 204 " ideal model delta sigma weight residual 124.31 134.19 -9.88 1.67e+00 3.59e-01 3.50e+01 angle pdb=" C ASN E 203 " pdb=" N GLN E 204 " pdb=" CA GLN E 204 " ideal model delta sigma weight residual 124.31 134.18 -9.87 1.67e+00 3.59e-01 3.49e+01 angle pdb=" C ASN A 203 " pdb=" N GLN A 204 " pdb=" CA GLN A 204 " ideal model delta sigma weight residual 124.31 134.16 -9.85 1.67e+00 3.59e-01 3.48e+01 angle pdb=" C ASN C 203 " pdb=" N GLN C 204 " pdb=" CA GLN C 204 " ideal model delta sigma weight residual 124.31 134.16 -9.85 1.67e+00 3.59e-01 3.48e+01 angle pdb=" CA GLU I 52 " pdb=" CB GLU I 52 " pdb=" CG GLU I 52 " ideal model delta sigma weight residual 114.10 125.85 -11.75 2.00e+00 2.50e-01 3.45e+01 ... (remaining 24005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 8930 15.67 - 31.34: 1326 31.34 - 47.00: 356 47.00 - 62.67: 112 62.67 - 78.34: 28 Dihedral angle restraints: 10752 sinusoidal: 4382 harmonic: 6370 Sorted by residual: dihedral pdb=" CB CYS B 160 " pdb=" SG CYS B 160 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.16 -72.16 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS G 160 " pdb=" SG CYS G 160 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.16 -72.16 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS A 160 " pdb=" SG CYS A 160 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual 93.00 165.15 -72.15 1 1.00e+01 1.00e-02 6.66e+01 ... (remaining 10749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1747 0.058 - 0.116: 714 0.116 - 0.175: 150 0.175 - 0.233: 35 0.233 - 0.291: 21 Chirality restraints: 2667 Sorted by residual: chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU N 63 " pdb=" CB LEU N 63 " pdb=" CD1 LEU N 63 " pdb=" CD2 LEU N 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU M 63 " pdb=" CB LEU M 63 " pdb=" CD1 LEU M 63 " pdb=" CD2 LEU M 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2664 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS M 124 " 0.015 2.00e-02 2.50e+03 2.11e-02 6.71e+00 pdb=" CG HIS M 124 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS M 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS M 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS M 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS M 124 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 124 " 0.015 2.00e-02 2.50e+03 2.11e-02 6.67e+00 pdb=" CG HIS K 124 " -0.045 2.00e-02 2.50e+03 pdb=" ND1 HIS K 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS K 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS K 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 124 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 124 " 0.015 2.00e-02 2.50e+03 2.10e-02 6.63e+00 pdb=" CG HIS L 124 " -0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS L 124 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS L 124 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS L 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS L 124 " 0.000 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4464 2.80 - 3.33: 14031 3.33 - 3.85: 28393 3.85 - 4.38: 32720 4.38 - 4.90: 58799 Nonbonded interactions: 138407 Sorted by model distance: nonbonded pdb=" OH TYR A 188 " pdb=" ND2 ASN H 127 " model vdw 2.277 2.520 nonbonded pdb=" O THR C 41 " pdb=" OG1 THR C 41 " model vdw 2.283 2.440 nonbonded pdb=" O THR G 41 " pdb=" OG1 THR G 41 " model vdw 2.283 2.440 nonbonded pdb=" O THR D 41 " pdb=" OG1 THR D 41 " model vdw 2.283 2.440 nonbonded pdb=" O THR F 41 " pdb=" OG1 THR F 41 " model vdw 2.283 2.440 ... (remaining 138402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 7.850 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 43.550 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 17738 Z= 0.439 Angle : 1.204 15.424 24010 Z= 0.608 Chirality : 0.068 0.291 2667 Planarity : 0.006 0.039 3066 Dihedral : 16.375 78.339 6545 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.05 % Allowed : 27.02 % Favored : 71.93 % 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: -1.46 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.35 (0.16), residues: 903 loop : -1.48 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.005 TRP D 34 HIS 0.027 0.003 HIS M 124 PHE 0.030 0.003 PHE N 56 TYR 0.025 0.003 TYR G 74 ARG 0.008 0.001 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 392 time to evaluate : 1.810 Fit side-chains REVERT: B 83 MET cc_start: 0.8012 (mmt) cc_final: 0.7597 (mpp) REVERT: B 88 ARG cc_start: 0.8734 (ptp-170) cc_final: 0.8494 (ptp90) REVERT: B 173 HIS cc_start: 0.8316 (m-70) cc_final: 0.7925 (m90) REVERT: D 83 MET cc_start: 0.8013 (mmt) cc_final: 0.7559 (mpp) REVERT: E 83 MET cc_start: 0.7906 (mmt) cc_final: 0.7433 (mpp) REVERT: F 83 MET cc_start: 0.7980 (mmt) cc_final: 0.7531 (mpp) REVERT: F 126 MET cc_start: 0.8532 (mmp) cc_final: 0.8316 (mmm) REVERT: F 213 SER cc_start: 0.8648 (p) cc_final: 0.8434 (m) REVERT: G 83 MET cc_start: 0.7999 (mmt) cc_final: 0.7611 (mpp) REVERT: H 50 LEU cc_start: 0.7873 (tt) cc_final: 0.7496 (tt) REVERT: H 74 LYS cc_start: 0.6836 (mtpp) cc_final: 0.6322 (mmtp) REVERT: I 50 LEU cc_start: 0.8022 (tt) cc_final: 0.7815 (tt) REVERT: L 50 LEU cc_start: 0.7414 (tt) cc_final: 0.7139 (tt) REVERT: L 63 LEU cc_start: 0.8093 (mm) cc_final: 0.7593 (mp) REVERT: N 50 LEU cc_start: 0.7929 (tt) cc_final: 0.7637 (tt) REVERT: N 63 LEU cc_start: 0.8531 (mm) cc_final: 0.8030 (mp) outliers start: 21 outliers final: 7 residues processed: 406 average time/residue: 0.3302 time to fit residues: 193.7540 Evaluate side-chains 273 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 266 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 162 ASN A 204 GLN B 79 ASN B 162 ASN B 179 ASN C 79 ASN C 162 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 162 ASN ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN E 162 ASN ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN F 79 ASN F 162 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN G 79 ASN G 162 ASN ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN H 124 HIS H 127 ASN I 109 GLN I 127 ASN ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 GLN J 127 ASN K 41 GLN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 HIS ** L 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 ASN ** M 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 ASN N 41 GLN ** N 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 127 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17738 Z= 0.234 Angle : 0.635 8.100 24010 Z= 0.327 Chirality : 0.047 0.164 2667 Planarity : 0.003 0.036 3066 Dihedral : 5.063 27.314 2352 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.86 % Allowed : 22.26 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2121 helix: None (None), residues: 0 sheet: -0.52 (0.16), residues: 966 loop : -1.22 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 34 HIS 0.009 0.001 HIS L 124 PHE 0.013 0.001 PHE H 56 TYR 0.012 0.001 TYR D 46 ARG 0.008 0.001 ARG N 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 258 time to evaluate : 1.822 Fit side-chains REVERT: B 83 MET cc_start: 0.8135 (mmt) cc_final: 0.7609 (mpp) REVERT: C 64 ASP cc_start: 0.7970 (t0) cc_final: 0.7743 (t0) REVERT: C 134 LYS cc_start: 0.8219 (tttt) cc_final: 0.8015 (ttpt) REVERT: E 185 ASN cc_start: 0.8629 (t0) cc_final: 0.8138 (t0) REVERT: F 64 ASP cc_start: 0.7749 (t0) cc_final: 0.7496 (t0) REVERT: F 213 SER cc_start: 0.8703 (p) cc_final: 0.8485 (m) REVERT: H 50 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7379 (tt) REVERT: H 65 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7775 (mp) REVERT: J 50 LEU cc_start: 0.7889 (tt) cc_final: 0.7604 (tt) REVERT: J 65 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7905 (mp) REVERT: K 126 MET cc_start: 0.6800 (ptm) cc_final: 0.6591 (ptm) REVERT: L 50 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7074 (tt) REVERT: N 50 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7346 (tt) outliers start: 117 outliers final: 61 residues processed: 338 average time/residue: 0.3172 time to fit residues: 161.9437 Evaluate side-chains 309 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 116 HIS C 79 ASN C 116 HIS ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 ASN D 116 HIS D 173 HIS ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 HIS G 173 HIS ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 41 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 GLN J 127 ASN L 41 GLN ** L 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN ** N 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17738 Z= 0.352 Angle : 0.667 7.878 24010 Z= 0.341 Chirality : 0.049 0.172 2667 Planarity : 0.003 0.029 3066 Dihedral : 5.126 37.886 2352 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.86 % Allowed : 20.35 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.61 (0.16), residues: 987 loop : -1.12 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 57 HIS 0.007 0.001 HIS L 124 PHE 0.012 0.001 PHE K 56 TYR 0.016 0.002 TYR D 46 ARG 0.014 0.001 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 306 time to evaluate : 2.021 Fit side-chains REVERT: A 64 ASP cc_start: 0.7820 (t0) cc_final: 0.7573 (t0) REVERT: A 83 MET cc_start: 0.8430 (mmm) cc_final: 0.8149 (mmm) REVERT: A 134 LYS cc_start: 0.8229 (tttt) cc_final: 0.7935 (ttpt) REVERT: B 64 ASP cc_start: 0.7971 (t0) cc_final: 0.7662 (t0) REVERT: C 64 ASP cc_start: 0.8120 (t0) cc_final: 0.7823 (t0) REVERT: C 134 LYS cc_start: 0.8293 (tttt) cc_final: 0.7976 (ttpt) REVERT: D 64 ASP cc_start: 0.8194 (t0) cc_final: 0.7872 (t0) REVERT: D 134 LYS cc_start: 0.8306 (tttt) cc_final: 0.8007 (ttpt) REVERT: E 64 ASP cc_start: 0.7940 (t0) cc_final: 0.7680 (t0) REVERT: E 134 LYS cc_start: 0.8243 (tttt) cc_final: 0.7970 (ttpt) REVERT: F 64 ASP cc_start: 0.7903 (t0) cc_final: 0.7652 (t0) REVERT: F 134 LYS cc_start: 0.8208 (tttt) cc_final: 0.7896 (ttpt) REVERT: G 64 ASP cc_start: 0.7964 (t0) cc_final: 0.7702 (t0) REVERT: G 114 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8202 (tppt) REVERT: G 134 LYS cc_start: 0.8298 (tttt) cc_final: 0.8047 (ttpt) REVERT: K 65 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8081 (mp) REVERT: K 126 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6636 (ptm) REVERT: M 50 LEU cc_start: 0.7906 (tt) cc_final: 0.7661 (tt) REVERT: N 50 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7674 (tt) outliers start: 117 outliers final: 78 residues processed: 388 average time/residue: 0.2810 time to fit residues: 165.2625 Evaluate side-chains 364 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 282 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 191 optimal weight: 9.9990 chunk 202 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN I 124 HIS ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 HIS ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17738 Z= 0.192 Angle : 0.587 7.532 24010 Z= 0.298 Chirality : 0.046 0.160 2667 Planarity : 0.003 0.029 3066 Dihedral : 4.813 38.623 2352 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.86 % Allowed : 21.20 % Favored : 73.93 % 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: -1.38 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.68 (0.16), residues: 973 loop : -1.06 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 57 HIS 0.005 0.001 HIS N 124 PHE 0.011 0.001 PHE H 56 TYR 0.016 0.001 TYR F 188 ARG 0.004 0.000 ARG J 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 306 time to evaluate : 1.772 Fit side-chains REVERT: A 64 ASP cc_start: 0.7832 (t0) cc_final: 0.7568 (t0) REVERT: A 134 LYS cc_start: 0.8133 (tttt) cc_final: 0.7823 (ttpt) REVERT: B 64 ASP cc_start: 0.7969 (t0) cc_final: 0.7663 (t0) REVERT: C 28 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7504 (ptm160) REVERT: C 64 ASP cc_start: 0.8104 (t0) cc_final: 0.7765 (t0) REVERT: C 134 LYS cc_start: 0.8255 (tttt) cc_final: 0.7962 (ttpt) REVERT: C 185 ASN cc_start: 0.8650 (t0) cc_final: 0.8183 (t0) REVERT: C 187 GLU cc_start: 0.8970 (pt0) cc_final: 0.8755 (pt0) REVERT: D 64 ASP cc_start: 0.8140 (t0) cc_final: 0.7772 (t0) REVERT: D 134 LYS cc_start: 0.8280 (tttt) cc_final: 0.7975 (ttpt) REVERT: E 64 ASP cc_start: 0.7951 (t0) cc_final: 0.7668 (t0) REVERT: E 85 THR cc_start: 0.8864 (p) cc_final: 0.8617 (p) REVERT: E 134 LYS cc_start: 0.8249 (tttt) cc_final: 0.7865 (ttpt) REVERT: F 64 ASP cc_start: 0.7918 (t0) cc_final: 0.7655 (t0) REVERT: F 134 LYS cc_start: 0.8179 (tttt) cc_final: 0.7797 (ttpt) REVERT: G 64 ASP cc_start: 0.7870 (t0) cc_final: 0.7590 (t0) REVERT: G 114 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8228 (tppt) REVERT: G 134 LYS cc_start: 0.8284 (tttt) cc_final: 0.7905 (ttpt) REVERT: K 126 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6696 (ptm) REVERT: M 130 LEU cc_start: 0.7072 (tp) cc_final: 0.6678 (tp) outliers start: 97 outliers final: 71 residues processed: 372 average time/residue: 0.2801 time to fit residues: 158.3099 Evaluate side-chains 363 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 289 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 114 LYS Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 0.0770 chunk 151 optimal weight: 10.0000 chunk 83 optimal weight: 0.0570 chunk 173 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 103 optimal weight: 0.0770 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 ASN ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17738 Z= 0.145 Angle : 0.562 7.996 24010 Z= 0.283 Chirality : 0.045 0.178 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.569 37.466 2352 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.66 % Allowed : 22.91 % Favored : 73.43 % 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: -1.30 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.64 (0.16), residues: 973 loop : -0.98 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 57 HIS 0.004 0.000 HIS M 124 PHE 0.013 0.001 PHE H 56 TYR 0.009 0.001 TYR G 46 ARG 0.004 0.000 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 296 time to evaluate : 1.991 Fit side-chains REVERT: A 64 ASP cc_start: 0.7792 (t0) cc_final: 0.7532 (t0) REVERT: B 64 ASP cc_start: 0.7949 (t0) cc_final: 0.7664 (t0) REVERT: C 28 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7536 (ptm160) REVERT: C 30 ASP cc_start: 0.7037 (p0) cc_final: 0.6834 (p0) REVERT: C 64 ASP cc_start: 0.8119 (t0) cc_final: 0.7755 (t0) REVERT: C 134 LYS cc_start: 0.8192 (tttt) cc_final: 0.7917 (ttpt) REVERT: C 185 ASN cc_start: 0.8628 (t0) cc_final: 0.8199 (t0) REVERT: D 64 ASP cc_start: 0.8138 (t0) cc_final: 0.7733 (t0) REVERT: D 134 LYS cc_start: 0.8210 (tttt) cc_final: 0.7914 (ttpt) REVERT: E 28 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7418 (ptm160) REVERT: E 30 ASP cc_start: 0.6927 (p0) cc_final: 0.6656 (p0) REVERT: E 64 ASP cc_start: 0.7908 (t0) cc_final: 0.7612 (t0) REVERT: E 85 THR cc_start: 0.8784 (p) cc_final: 0.8457 (p) REVERT: E 134 LYS cc_start: 0.8254 (tttt) cc_final: 0.7882 (ttpt) REVERT: F 64 ASP cc_start: 0.7906 (t0) cc_final: 0.7655 (t0) REVERT: F 134 LYS cc_start: 0.8168 (tttt) cc_final: 0.7752 (ttpt) REVERT: F 213 SER cc_start: 0.8828 (p) cc_final: 0.8623 (m) REVERT: G 64 ASP cc_start: 0.7853 (t0) cc_final: 0.7551 (t0) REVERT: G 83 MET cc_start: 0.8352 (mmt) cc_final: 0.7746 (mpp) REVERT: G 134 LYS cc_start: 0.8253 (tttt) cc_final: 0.7900 (ttpt) REVERT: K 65 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8076 (mp) REVERT: K 126 MET cc_start: 0.6966 (ptm) cc_final: 0.6741 (ptm) outliers start: 73 outliers final: 50 residues processed: 347 average time/residue: 0.2953 time to fit residues: 153.7225 Evaluate side-chains 336 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 283 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 168 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN I 46 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN L 124 HIS ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17738 Z= 0.235 Angle : 0.591 9.030 24010 Z= 0.295 Chirality : 0.046 0.158 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.635 40.696 2352 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 5.26 % Allowed : 21.55 % Favored : 73.18 % 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: -1.31 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.60 (0.16), residues: 945 loop : -1.05 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 57 HIS 0.004 0.001 HIS L 124 PHE 0.011 0.001 PHE L 56 TYR 0.015 0.001 TYR D 46 ARG 0.003 0.000 ARG M 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 283 time to evaluate : 2.030 Fit side-chains REVERT: A 64 ASP cc_start: 0.7905 (t0) cc_final: 0.7658 (t0) REVERT: B 64 ASP cc_start: 0.8015 (t0) cc_final: 0.7723 (t0) REVERT: C 64 ASP cc_start: 0.8150 (t0) cc_final: 0.7776 (t0) REVERT: C 134 LYS cc_start: 0.8304 (tttt) cc_final: 0.7987 (ttpt) REVERT: D 64 ASP cc_start: 0.8208 (t0) cc_final: 0.7778 (t0) REVERT: D 134 LYS cc_start: 0.8313 (tttt) cc_final: 0.7946 (ttpt) REVERT: E 64 ASP cc_start: 0.7941 (t0) cc_final: 0.7657 (t0) REVERT: E 85 THR cc_start: 0.8884 (p) cc_final: 0.8661 (p) REVERT: E 134 LYS cc_start: 0.8372 (tttt) cc_final: 0.7897 (ttpt) REVERT: F 64 ASP cc_start: 0.7946 (t0) cc_final: 0.7688 (t0) REVERT: F 134 LYS cc_start: 0.8243 (tttt) cc_final: 0.7783 (ttpt) REVERT: G 64 ASP cc_start: 0.7946 (t0) cc_final: 0.7646 (t0) REVERT: G 134 LYS cc_start: 0.8396 (tttt) cc_final: 0.7916 (ttpt) REVERT: K 65 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8116 (mp) REVERT: K 126 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6753 (ptm) outliers start: 105 outliers final: 81 residues processed: 362 average time/residue: 0.3091 time to fit residues: 171.7913 Evaluate side-chains 356 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 273 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17738 Z= 0.216 Angle : 0.585 9.693 24010 Z= 0.290 Chirality : 0.045 0.149 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.591 41.799 2352 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 4.76 % Allowed : 22.06 % Favored : 73.18 % 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: -1.31 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.55 (0.17), residues: 875 loop : -1.08 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 57 HIS 0.003 0.001 HIS M 124 PHE 0.011 0.001 PHE L 56 TYR 0.013 0.001 TYR D 46 ARG 0.003 0.000 ARG M 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 273 time to evaluate : 1.862 Fit side-chains REVERT: A 64 ASP cc_start: 0.7893 (t0) cc_final: 0.7648 (t0) REVERT: B 64 ASP cc_start: 0.8024 (t0) cc_final: 0.7733 (t0) REVERT: C 64 ASP cc_start: 0.8161 (t0) cc_final: 0.7793 (t0) REVERT: C 134 LYS cc_start: 0.8309 (tttt) cc_final: 0.7969 (ttpt) REVERT: D 64 ASP cc_start: 0.8227 (t0) cc_final: 0.7792 (t0) REVERT: D 134 LYS cc_start: 0.8298 (tttt) cc_final: 0.7942 (ttpt) REVERT: E 64 ASP cc_start: 0.7910 (t0) cc_final: 0.7646 (t0) REVERT: E 85 THR cc_start: 0.8913 (p) cc_final: 0.8648 (p) REVERT: E 134 LYS cc_start: 0.8291 (tttt) cc_final: 0.7818 (ttpt) REVERT: F 64 ASP cc_start: 0.7968 (t0) cc_final: 0.7707 (t0) REVERT: F 134 LYS cc_start: 0.8223 (tttt) cc_final: 0.7769 (ttpt) REVERT: G 64 ASP cc_start: 0.7994 (t0) cc_final: 0.7687 (t0) REVERT: G 134 LYS cc_start: 0.8369 (tttt) cc_final: 0.7902 (ttpt) REVERT: I 126 MET cc_start: 0.7045 (ptm) cc_final: 0.6831 (ptm) REVERT: K 65 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8116 (mp) REVERT: K 126 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6722 (ptm) outliers start: 95 outliers final: 80 residues processed: 345 average time/residue: 0.2901 time to fit residues: 150.8163 Evaluate side-chains 353 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 271 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.0670 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 HIS ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17738 Z= 0.193 Angle : 0.578 10.306 24010 Z= 0.286 Chirality : 0.045 0.156 2667 Planarity : 0.003 0.027 3066 Dihedral : 4.511 41.566 2352 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.41 % Allowed : 22.26 % Favored : 73.33 % 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: -1.26 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.51 (0.17), residues: 875 loop : -1.06 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 57 HIS 0.004 0.001 HIS M 124 PHE 0.011 0.001 PHE L 56 TYR 0.012 0.001 TYR D 46 ARG 0.003 0.000 ARG H 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 275 time to evaluate : 1.960 Fit side-chains REVERT: A 64 ASP cc_start: 0.7891 (t0) cc_final: 0.7649 (t0) REVERT: B 64 ASP cc_start: 0.8024 (t0) cc_final: 0.7732 (t0) REVERT: C 28 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7237 (ptm160) REVERT: C 64 ASP cc_start: 0.8167 (t0) cc_final: 0.7787 (t0) REVERT: C 134 LYS cc_start: 0.8239 (tttt) cc_final: 0.7883 (ttpt) REVERT: D 64 ASP cc_start: 0.8227 (t0) cc_final: 0.7786 (t0) REVERT: D 134 LYS cc_start: 0.8311 (tttt) cc_final: 0.7979 (ttpt) REVERT: E 28 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7398 (ptm160) REVERT: E 30 ASP cc_start: 0.6830 (p0) cc_final: 0.6530 (p0) REVERT: E 64 ASP cc_start: 0.7920 (t0) cc_final: 0.7656 (t0) REVERT: E 85 THR cc_start: 0.8946 (p) cc_final: 0.8737 (p) REVERT: E 134 LYS cc_start: 0.8277 (tttt) cc_final: 0.7810 (ttpt) REVERT: F 64 ASP cc_start: 0.7972 (t0) cc_final: 0.7713 (t0) REVERT: F 134 LYS cc_start: 0.8185 (tttt) cc_final: 0.7755 (ttpt) REVERT: F 213 SER cc_start: 0.8853 (p) cc_final: 0.8651 (m) REVERT: G 64 ASP cc_start: 0.7995 (t0) cc_final: 0.7684 (t0) REVERT: G 134 LYS cc_start: 0.8369 (tttt) cc_final: 0.7966 (ttpt) REVERT: K 65 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8097 (mp) REVERT: K 126 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6799 (ptm) REVERT: L 83 MET cc_start: 0.7210 (tpp) cc_final: 0.6914 (tpp) REVERT: M 83 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7367 (tpp) outliers start: 88 outliers final: 76 residues processed: 342 average time/residue: 0.2966 time to fit residues: 153.3169 Evaluate side-chains 349 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 268 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 HIS F 116 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 124 HIS ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17738 Z= 0.359 Angle : 0.647 10.941 24010 Z= 0.322 Chirality : 0.048 0.181 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.826 38.238 2352 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.45 % Favored : 92.46 % Rotamer: Outliers : 4.71 % Allowed : 22.31 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.74 (0.16), residues: 959 loop : -1.10 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 57 HIS 0.005 0.001 HIS D 117 PHE 0.012 0.001 PHE J 56 TYR 0.019 0.002 TYR D 46 ARG 0.004 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 251 time to evaluate : 2.087 Fit side-chains REVERT: A 64 ASP cc_start: 0.8014 (t0) cc_final: 0.7764 (t0) REVERT: A 83 MET cc_start: 0.8581 (mmm) cc_final: 0.8089 (mmm) REVERT: B 64 ASP cc_start: 0.8176 (t0) cc_final: 0.7856 (t0) REVERT: C 64 ASP cc_start: 0.8265 (t0) cc_final: 0.7873 (t0) REVERT: C 134 LYS cc_start: 0.8363 (tttt) cc_final: 0.7955 (ttpt) REVERT: D 64 ASP cc_start: 0.8260 (t0) cc_final: 0.7818 (t0) REVERT: D 134 LYS cc_start: 0.8319 (tttt) cc_final: 0.7964 (ttpt) REVERT: E 64 ASP cc_start: 0.7978 (t0) cc_final: 0.7722 (t0) REVERT: E 134 LYS cc_start: 0.8399 (tttt) cc_final: 0.7905 (ttpt) REVERT: F 64 ASP cc_start: 0.8058 (t0) cc_final: 0.7782 (t0) REVERT: F 134 LYS cc_start: 0.8291 (tttt) cc_final: 0.7851 (ttpt) REVERT: G 64 ASP cc_start: 0.8090 (t0) cc_final: 0.7804 (t0) REVERT: G 134 LYS cc_start: 0.8456 (tttt) cc_final: 0.8031 (ttpt) REVERT: I 83 MET cc_start: 0.7105 (mmm) cc_final: 0.6880 (mmm) REVERT: K 65 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8203 (mp) REVERT: K 126 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6741 (ptm) REVERT: L 83 MET cc_start: 0.7242 (tpp) cc_final: 0.6856 (tpp) REVERT: M 83 MET cc_start: 0.7749 (mmt) cc_final: 0.7508 (tpp) outliers start: 94 outliers final: 80 residues processed: 330 average time/residue: 0.2898 time to fit residues: 144.7821 Evaluate side-chains 327 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 245 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Chi-restraints excluded: chain N residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 138 optimal weight: 0.0870 chunk 209 optimal weight: 0.8980 chunk 192 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17738 Z= 0.195 Angle : 0.595 11.550 24010 Z= 0.292 Chirality : 0.046 0.158 2667 Planarity : 0.003 0.029 3066 Dihedral : 4.578 35.277 2352 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 3.61 % Allowed : 23.56 % Favored : 72.83 % 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: -1.39 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.72 (0.17), residues: 945 loop : -1.04 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 57 HIS 0.003 0.001 HIS K 79 PHE 0.011 0.001 PHE L 56 TYR 0.011 0.001 TYR D 46 ARG 0.003 0.000 ARG M 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 246 time to evaluate : 2.066 Fit side-chains REVERT: A 64 ASP cc_start: 0.7949 (t0) cc_final: 0.7710 (t0) REVERT: B 64 ASP cc_start: 0.8133 (t0) cc_final: 0.7833 (t0) REVERT: C 28 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7289 (ptm160) REVERT: C 64 ASP cc_start: 0.8172 (t0) cc_final: 0.7806 (t0) REVERT: C 134 LYS cc_start: 0.8302 (tttt) cc_final: 0.7887 (ttpt) REVERT: D 64 ASP cc_start: 0.8223 (t0) cc_final: 0.7797 (t0) REVERT: D 134 LYS cc_start: 0.8256 (tttt) cc_final: 0.7933 (ttpt) REVERT: E 28 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7551 (ptm160) REVERT: E 64 ASP cc_start: 0.7962 (t0) cc_final: 0.7706 (t0) REVERT: E 134 LYS cc_start: 0.8298 (tttt) cc_final: 0.7815 (ttpt) REVERT: F 64 ASP cc_start: 0.8016 (t0) cc_final: 0.7738 (t0) REVERT: F 134 LYS cc_start: 0.8186 (tttt) cc_final: 0.7831 (ttpt) REVERT: G 64 ASP cc_start: 0.8055 (t0) cc_final: 0.7757 (t0) REVERT: G 134 LYS cc_start: 0.8305 (tttt) cc_final: 0.7902 (ttpt) REVERT: K 65 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8168 (mp) REVERT: K 126 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6767 (ptm) REVERT: L 83 MET cc_start: 0.7203 (tpp) cc_final: 0.6854 (tpp) REVERT: M 83 MET cc_start: 0.7656 (mmt) cc_final: 0.7377 (tpp) outliers start: 72 outliers final: 65 residues processed: 306 average time/residue: 0.3139 time to fit residues: 144.0980 Evaluate side-chains 317 residues out of total 1995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 248 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 28 ARG Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 ASP Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 126 MET Chi-restraints excluded: chain M residue 107 LEU Chi-restraints excluded: chain N residue 107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0670 chunk 51 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.0010 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 21 optimal weight: 0.0010 chunk 30 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.3730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.202170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148804 restraints weight = 20461.358| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.17 r_work: 0.3444 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1015 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1008 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17738 Z= 0.156 Angle : 0.585 11.787 24010 Z= 0.286 Chirality : 0.045 0.158 2667 Planarity : 0.003 0.028 3066 Dihedral : 4.295 29.402 2352 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.88 % Favored : 92.98 % Rotamer: Outliers : 3.26 % Allowed : 23.96 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2121 helix: None (None), residues: 0 sheet: -0.53 (0.17), residues: 875 loop : -1.03 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 57 HIS 0.002 0.000 HIS J 79 PHE 0.011 0.001 PHE L 56 TYR 0.017 0.001 TYR E 188 ARG 0.003 0.000 ARG M 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4406.50 seconds wall clock time: 80 minutes 34.18 seconds (4834.18 seconds total)