Starting phenix.real_space_refine on Sat Feb 17 01:21:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfg_23816/02_2024/7mfg_23816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfg_23816/02_2024/7mfg_23816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfg_23816/02_2024/7mfg_23816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfg_23816/02_2024/7mfg_23816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfg_23816/02_2024/7mfg_23816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfg_23816/02_2024/7mfg_23816.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 10674 2.51 5 N 2865 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17013 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1274 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "C" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1274 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "E" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1274 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 1, 'TRANS': 155} Chain: "J" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 9.44, per 1000 atoms: 0.55 Number of scatterers: 17013 At special positions: 0 Unit cell: (138.449, 137.376, 145.962, 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 87 16.00 O 3387 8.00 N 2865 7.00 C 10674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS I 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 63 " " NAG A 403 " - " ASN A 129 " " NAG A 404 " - " ASN A 94 " " NAG A 405 " - " ASN A 33 " " NAG A 406 " - " ASN A 289 " " NAG A 407 " - " ASN A 163 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 63 " " NAG C 403 " - " ASN C 129 " " NAG C 404 " - " ASN C 94 " " NAG C 405 " - " ASN C 33 " " NAG C 406 " - " ASN C 289 " " NAG C 407 " - " ASN C 163 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 63 " " NAG G 403 " - " ASN G 129 " " NAG G 404 " - " ASN G 94 " " NAG G 405 " - " ASN G 33 " " NAG G 406 " - " ASN G 289 " " NAG G 407 " - " ASN G 163 " " NAG M 1 " - " ASN B 154 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN I 154 " Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 2.9 seconds 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3858 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 20.7% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 77 through 81A removed outlier: 4.300A pdb=" N SER A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 81A" --> pdb=" O LEU A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 81A' Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.595A pdb=" N GLU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.069A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.632A pdb=" N CYS B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 126 removed outlier: 3.558A pdb=" N ASP B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 77 through 81A removed outlier: 4.311A pdb=" N SER C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 81A" --> pdb=" O LEU C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 81A' Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.609A pdb=" N GLU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.047A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.623A pdb=" N CYS D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.534A pdb=" N ASP D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 77 through 81A removed outlier: 4.302A pdb=" N SER G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS G 81A" --> pdb=" O LEU G 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 77 through 81A' Processing helix chain 'G' and resid 104 through 114 removed outlier: 3.609A pdb=" N GLU G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER G 114 " --> pdb=" O GLU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 4.072A pdb=" N TRP G 127 " --> pdb=" O LYS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 160 No H-bonds generated for 'chain 'G' and resid 158 through 160' Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 37 through 59 removed outlier: 3.615A pdb=" N CYS I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 74 through 126 removed outlier: 3.550A pdb=" N ASP I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 162 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.590A pdb=" N ALA B 35 " --> pdb=" O TYR B 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.155A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.535A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 118 removed outlier: 4.011A pdb=" N SER A 116A" --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 259 " --> pdb=" O GLU A 116C" (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA9, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.516A pdb=" N VAL A 202 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 204 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 209 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.697A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN H 58 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.697A pdb=" N GLU H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.321A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.235A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.601A pdb=" N ALA D 35 " --> pdb=" O TYR D 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.157A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.521A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.993A pdb=" N SER C 116A" --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 259 " --> pdb=" O GLU C 116C" (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC7, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC8, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.524A pdb=" N VAL C 204 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AD1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.691A pdb=" N GLU E 10 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 110 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 37 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA E 93 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN E 58 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.691A pdb=" N GLU E 10 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 110 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.318A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.232A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 35 through 36 removed outlier: 3.612A pdb=" N ALA I 35 " --> pdb=" O TYR I 24 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 24 through 26 removed outlier: 4.173A pdb=" N ASP G 24 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.531A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 115 through 118 removed outlier: 4.003A pdb=" N SER G 116A" --> pdb=" O SER G 261 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA G 259 " --> pdb=" O GLU G 116C" (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 176 " --> pdb=" O LEU G 237 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 130 through 131 Processing sheet with id=AE6, first strand: chain 'G' and resid 151 through 153 Processing sheet with id=AE7, first strand: chain 'G' and resid 164 through 169 removed outlier: 3.868A pdb=" N TYR G 209 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AE9, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.696A pdb=" N GLU J 10 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN J 58 " --> pdb=" O GLY J 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.696A pdb=" N GLU J 10 " --> pdb=" O LEU J 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR J 110 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AF4, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.303A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.218A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1497 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: 5.48 Time building geometry restraints manager: 7.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5496 1.34 - 1.46: 4317 1.46 - 1.58: 7476 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 17409 Sorted by residual: bond pdb=" N GLU K 1 " pdb=" CA GLU K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP C 11 " pdb=" CA ASP C 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N GLU L 1 " pdb=" CA GLU L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N ASP A 11 " pdb=" CA ASP A 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 ... (remaining 17404 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.24: 556 107.24 - 113.93: 9655 113.93 - 120.62: 6541 120.62 - 127.32: 6624 127.32 - 134.01: 213 Bond angle restraints: 23589 Sorted by residual: angle pdb=" N TRP G 255 " pdb=" CA TRP G 255 " pdb=" C TRP G 255 " ideal model delta sigma weight residual 114.04 109.38 4.66 1.24e+00 6.50e-01 1.41e+01 angle pdb=" N ASN A 289 " pdb=" CA ASN A 289 " pdb=" CB ASN A 289 " ideal model delta sigma weight residual 113.65 109.97 3.68 1.47e+00 4.63e-01 6.27e+00 angle pdb=" N ASN G 289 " pdb=" CA ASN G 289 " pdb=" CB ASN G 289 " ideal model delta sigma weight residual 113.65 109.98 3.67 1.47e+00 4.63e-01 6.23e+00 angle pdb=" N ASN C 289 " pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " ideal model delta sigma weight residual 113.65 110.00 3.65 1.47e+00 4.63e-01 6.17e+00 angle pdb=" N GLY E 52A" pdb=" CA GLY E 52A" pdb=" C GLY E 52A" ideal model delta sigma weight residual 111.78 115.94 -4.16 1.69e+00 3.50e-01 6.05e+00 ... (remaining 23584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 10272 21.71 - 43.41: 307 43.41 - 65.12: 72 65.12 - 86.83: 23 86.83 - 108.54: 15 Dihedral angle restraints: 10689 sinusoidal: 4611 harmonic: 6078 Sorted by residual: dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.83 108.54 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.81 108.52 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.80 108.51 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 10686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2255 0.054 - 0.108: 246 0.108 - 0.162: 97 0.162 - 0.217: 0 0.217 - 0.271: 3 Chirality restraints: 2601 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2598 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 323 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 324 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 323 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO C 324 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 324 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 323 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO G 324 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 324 " 0.021 5.00e-02 4.00e+02 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 209 2.57 - 3.16: 14681 3.16 - 3.74: 24334 3.74 - 4.32: 33966 4.32 - 4.90: 58455 Nonbonded interactions: 131645 Sorted by model distance: nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 22 " model vdw 1.993 2.440 nonbonded pdb=" OG SER F 7 " pdb=" OG SER F 22 " model vdw 1.999 2.440 nonbonded pdb=" OG SER K 7 " pdb=" OG SER K 22 " model vdw 2.018 2.440 nonbonded pdb=" O CYS A 305 " pdb=" OG1 THR B 61 " model vdw 2.085 2.440 nonbonded pdb=" O CYS C 305 " pdb=" OG1 THR D 61 " model vdw 2.085 2.440 ... (remaining 131640 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 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 7.290 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 45.720 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17409 Z= 0.184 Angle : 0.471 6.236 23589 Z= 0.236 Chirality : 0.042 0.271 2601 Planarity : 0.003 0.042 3018 Dihedral : 11.844 108.537 6750 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.22 % Allowed : 2.25 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2097 helix: 3.16 (0.28), residues: 327 sheet: 0.60 (0.27), residues: 411 loop : -0.57 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.000 HIS J 101 PHE 0.007 0.001 PHE C 213 TYR 0.005 0.001 TYR A 101 ARG 0.002 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.8885 (mtp) cc_final: 0.8412 (ttp) REVERT: B 59 MET cc_start: 0.9235 (mmm) cc_final: 0.9028 (mmm) REVERT: B 85 ASP cc_start: 0.9177 (m-30) cc_final: 0.8837 (m-30) REVERT: B 112 ASP cc_start: 0.9353 (m-30) cc_final: 0.9141 (m-30) REVERT: B 149 MET cc_start: 0.8814 (mmt) cc_final: 0.8406 (mmt) REVERT: H 45 LEU cc_start: 0.8422 (mp) cc_final: 0.8181 (mt) REVERT: H 80 MET cc_start: 0.7829 (tpp) cc_final: 0.6443 (tpp) REVERT: L 48 MET cc_start: 0.8587 (tpp) cc_final: 0.7985 (mmm) REVERT: C 316 MET cc_start: 0.8832 (mtp) cc_final: 0.8518 (ttp) REVERT: D 85 ASP cc_start: 0.9226 (m-30) cc_final: 0.8865 (m-30) REVERT: D 112 ASP cc_start: 0.9424 (m-30) cc_final: 0.9223 (m-30) REVERT: D 149 MET cc_start: 0.8832 (mmt) cc_final: 0.8258 (mmt) REVERT: E 80 MET cc_start: 0.7841 (tpp) cc_final: 0.6633 (tpp) REVERT: F 48 MET cc_start: 0.8539 (tpp) cc_final: 0.7949 (mmm) REVERT: G 316 MET cc_start: 0.8893 (mtp) cc_final: 0.8644 (ttp) REVERT: I 38 GLN cc_start: 0.9123 (mt0) cc_final: 0.8908 (mm-40) REVERT: I 59 MET cc_start: 0.9206 (mmm) cc_final: 0.8709 (mmm) REVERT: I 85 ASP cc_start: 0.9232 (m-30) cc_final: 0.8920 (m-30) REVERT: I 112 ASP cc_start: 0.9333 (m-30) cc_final: 0.9116 (m-30) REVERT: I 149 MET cc_start: 0.8860 (mmt) cc_final: 0.8295 (mmt) REVERT: J 80 MET cc_start: 0.7915 (tpp) cc_final: 0.6528 (tpp) REVERT: K 48 MET cc_start: 0.8511 (tpp) cc_final: 0.7894 (mmm) REVERT: K 67 PHE cc_start: 0.8551 (p90) cc_final: 0.8198 (p90) outliers start: 4 outliers final: 4 residues processed: 221 average time/residue: 0.3408 time to fit residues: 107.9420 Evaluate side-chains 125 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain I residue 148 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN H 101 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 GLN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 64 GLN K 38 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 17409 Z= 0.615 Angle : 0.806 8.581 23589 Z= 0.419 Chirality : 0.048 0.172 2601 Planarity : 0.006 0.065 3018 Dihedral : 9.198 58.461 2926 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.20 % Allowed : 6.59 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2097 helix: 2.07 (0.27), residues: 336 sheet: -0.24 (0.25), residues: 432 loop : -0.92 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 103 HIS 0.007 0.002 HIS D 25 PHE 0.026 0.003 PHE G 118 TYR 0.016 0.003 TYR D 34 ARG 0.006 0.001 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.9394 (mmm) cc_final: 0.9026 (mmm) REVERT: B 85 ASP cc_start: 0.9127 (m-30) cc_final: 0.8672 (m-30) REVERT: B 89 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9366 (tt) REVERT: B 98 LEU cc_start: 0.9719 (tp) cc_final: 0.9467 (tt) REVERT: B 149 MET cc_start: 0.8780 (mmt) cc_final: 0.8340 (mmt) REVERT: H 80 MET cc_start: 0.7871 (tpp) cc_final: 0.7394 (tpp) REVERT: L 48 MET cc_start: 0.8768 (tpp) cc_final: 0.8340 (mmm) REVERT: L 49 TYR cc_start: 0.9427 (p90) cc_final: 0.9146 (p90) REVERT: D 149 MET cc_start: 0.8904 (mmt) cc_final: 0.8489 (mmt) REVERT: E 48 MET cc_start: 0.9174 (mmm) cc_final: 0.8857 (mmm) REVERT: F 48 MET cc_start: 0.8736 (tpp) cc_final: 0.8273 (mmm) REVERT: F 49 TYR cc_start: 0.9392 (p90) cc_final: 0.9035 (p90) REVERT: I 59 MET cc_start: 0.9461 (mmm) cc_final: 0.9180 (mmm) REVERT: I 85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8816 (m-30) REVERT: I 103 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7915 (tm-30) REVERT: I 149 MET cc_start: 0.8976 (mmt) cc_final: 0.8461 (mmm) REVERT: J 45 LEU cc_start: 0.8848 (mt) cc_final: 0.8588 (mt) REVERT: J 80 MET cc_start: 0.7481 (tpp) cc_final: 0.7139 (tpp) REVERT: K 48 MET cc_start: 0.8708 (tpp) cc_final: 0.8054 (mmm) REVERT: K 67 PHE cc_start: 0.8823 (p90) cc_final: 0.8393 (p90) outliers start: 40 outliers final: 22 residues processed: 161 average time/residue: 0.3223 time to fit residues: 76.7953 Evaluate side-chains 133 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 0.0000 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 282 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17409 Z= 0.246 Angle : 0.580 6.790 23589 Z= 0.299 Chirality : 0.043 0.170 2601 Planarity : 0.005 0.057 3018 Dihedral : 7.892 58.770 2925 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.09 % Allowed : 8.73 % Favored : 89.18 % 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: -0.13 (0.18), residues: 2097 helix: 2.40 (0.28), residues: 339 sheet: 0.28 (0.26), residues: 399 loop : -0.89 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 35 HIS 0.003 0.001 HIS I 25 PHE 0.018 0.001 PHE E 63 TYR 0.015 0.001 TYR I 94 ARG 0.008 0.001 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.9343 (mmm) cc_final: 0.9099 (mmm) REVERT: L 48 MET cc_start: 0.8708 (tpp) cc_final: 0.8193 (mmm) REVERT: L 49 TYR cc_start: 0.9473 (p90) cc_final: 0.9162 (p90) REVERT: D 77 MET cc_start: 0.8185 (mmt) cc_final: 0.7516 (mmt) REVERT: D 109 ASP cc_start: 0.9382 (m-30) cc_final: 0.9130 (p0) REVERT: D 149 MET cc_start: 0.8928 (mmt) cc_final: 0.8506 (mmt) REVERT: F 48 MET cc_start: 0.8641 (tpp) cc_final: 0.8079 (mmm) REVERT: F 49 TYR cc_start: 0.9386 (p90) cc_final: 0.9157 (p90) REVERT: G 116 PHE cc_start: 0.8697 (m-10) cc_final: 0.8446 (m-10) REVERT: G 275 ASP cc_start: 0.7862 (t0) cc_final: 0.7508 (t0) REVERT: I 59 MET cc_start: 0.9385 (mmm) cc_final: 0.9166 (mmm) REVERT: I 85 ASP cc_start: 0.9227 (m-30) cc_final: 0.8882 (m-30) REVERT: I 109 ASP cc_start: 0.9413 (m-30) cc_final: 0.9194 (p0) REVERT: I 149 MET cc_start: 0.9053 (mmt) cc_final: 0.8631 (mmt) REVERT: K 48 MET cc_start: 0.8551 (tpp) cc_final: 0.7856 (mmm) REVERT: K 67 PHE cc_start: 0.8763 (p90) cc_final: 0.8240 (p90) REVERT: K 100 GLN cc_start: 0.7519 (pp30) cc_final: 0.7302 (pp30) outliers start: 38 outliers final: 33 residues processed: 153 average time/residue: 0.3179 time to fit residues: 73.4765 Evaluate side-chains 144 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17409 Z= 0.300 Angle : 0.575 6.792 23589 Z= 0.297 Chirality : 0.042 0.170 2601 Planarity : 0.004 0.059 3018 Dihedral : 7.334 59.510 2925 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.75 % Allowed : 9.50 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2097 helix: 2.37 (0.28), residues: 339 sheet: 0.21 (0.26), residues: 411 loop : -0.88 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.003 0.001 HIS B 25 PHE 0.014 0.001 PHE G 213 TYR 0.010 0.001 TYR B 34 ARG 0.007 0.000 ARG F 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 59 MET cc_start: 0.9397 (mmm) cc_final: 0.9182 (mmm) REVERT: H 80 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7283 (tpp) REVERT: L 48 MET cc_start: 0.8620 (tpp) cc_final: 0.8159 (mmm) REVERT: L 49 TYR cc_start: 0.9482 (p90) cc_final: 0.9142 (p90) REVERT: C 217 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8588 (mp) REVERT: D 17 MET cc_start: 0.8441 (ttp) cc_final: 0.7999 (tmm) REVERT: D 109 ASP cc_start: 0.9414 (m-30) cc_final: 0.9150 (p0) REVERT: D 149 MET cc_start: 0.8967 (mmt) cc_final: 0.8560 (mmt) REVERT: F 48 MET cc_start: 0.8695 (tpp) cc_final: 0.8201 (mmm) REVERT: G 116 PHE cc_start: 0.8785 (m-10) cc_final: 0.8573 (m-10) REVERT: G 217 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8640 (mp) REVERT: G 275 ASP cc_start: 0.7921 (t0) cc_final: 0.7533 (t0) REVERT: I 85 ASP cc_start: 0.9217 (m-30) cc_final: 0.8853 (m-30) REVERT: I 109 ASP cc_start: 0.9425 (m-30) cc_final: 0.9209 (p0) REVERT: I 149 MET cc_start: 0.9075 (mmt) cc_final: 0.8567 (mmm) REVERT: K 48 MET cc_start: 0.8534 (tpp) cc_final: 0.7880 (mmm) REVERT: K 100 GLN cc_start: 0.7684 (pp30) cc_final: 0.7481 (pp30) outliers start: 50 outliers final: 36 residues processed: 157 average time/residue: 0.3030 time to fit residues: 72.0397 Evaluate side-chains 153 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 113 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.0470 chunk 113 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 3.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17409 Z= 0.284 Angle : 0.569 8.215 23589 Z= 0.290 Chirality : 0.042 0.166 2601 Planarity : 0.004 0.059 3018 Dihedral : 6.931 59.675 2924 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.91 % Allowed : 10.60 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2097 helix: 2.36 (0.28), residues: 339 sheet: 0.22 (0.26), residues: 411 loop : -0.93 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.003 0.001 HIS D 25 PHE 0.014 0.001 PHE C 213 TYR 0.011 0.001 TYR B 34 ARG 0.004 0.000 ARG G 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 114 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8590 (mp) REVERT: L 48 MET cc_start: 0.8622 (tpp) cc_final: 0.8108 (mmm) REVERT: L 77 ARG cc_start: 0.8803 (mpp80) cc_final: 0.8347 (mpp80) REVERT: C 217 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 260 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9254 (pp) REVERT: D 17 MET cc_start: 0.8393 (ttp) cc_final: 0.7913 (tmm) REVERT: D 109 ASP cc_start: 0.9396 (m-30) cc_final: 0.9128 (p0) REVERT: D 149 MET cc_start: 0.8986 (mmt) cc_final: 0.8646 (mmm) REVERT: F 48 MET cc_start: 0.8658 (tpp) cc_final: 0.8431 (tpp) REVERT: G 116 PHE cc_start: 0.8759 (m-10) cc_final: 0.8510 (m-10) REVERT: G 217 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8656 (mp) REVERT: G 275 ASP cc_start: 0.8008 (t0) cc_final: 0.7665 (t0) REVERT: I 59 MET cc_start: 0.9477 (mmm) cc_final: 0.9062 (mmm) REVERT: I 85 ASP cc_start: 0.9211 (m-30) cc_final: 0.8872 (m-30) REVERT: I 109 ASP cc_start: 0.9434 (m-30) cc_final: 0.9226 (p0) REVERT: I 149 MET cc_start: 0.9106 (mmt) cc_final: 0.8606 (mmm) REVERT: J 80 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7256 (tpp) REVERT: K 48 MET cc_start: 0.8515 (tpp) cc_final: 0.7880 (mmm) REVERT: K 77 ARG cc_start: 0.8997 (mpp80) cc_final: 0.8514 (mpp80) REVERT: K 100 GLN cc_start: 0.7797 (pp30) cc_final: 0.7568 (pp30) outliers start: 53 outliers final: 41 residues processed: 160 average time/residue: 0.2900 time to fit residues: 71.5027 Evaluate side-chains 157 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 111 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 144 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17409 Z= 0.348 Angle : 0.602 8.277 23589 Z= 0.308 Chirality : 0.042 0.167 2601 Planarity : 0.004 0.058 3018 Dihedral : 6.754 59.490 2922 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.19 % Allowed : 11.97 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2097 helix: 2.24 (0.28), residues: 339 sheet: 0.13 (0.26), residues: 411 loop : -1.03 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 103 HIS 0.003 0.001 HIS E 101 PHE 0.014 0.002 PHE C 213 TYR 0.011 0.001 TYR I 34 ARG 0.006 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 110 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8575 (mp) REVERT: B 89 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9381 (tt) REVERT: H 80 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7271 (tpp) REVERT: L 77 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8323 (mpp80) REVERT: C 217 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8571 (mp) REVERT: C 260 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9307 (pp) REVERT: D 17 MET cc_start: 0.8314 (ttp) cc_final: 0.7905 (tmm) REVERT: D 109 ASP cc_start: 0.9399 (m-30) cc_final: 0.9195 (p0) REVERT: D 149 MET cc_start: 0.9011 (mmt) cc_final: 0.8681 (mmm) REVERT: E 48 MET cc_start: 0.8947 (mmm) cc_final: 0.7940 (mtt) REVERT: F 48 MET cc_start: 0.8696 (tpp) cc_final: 0.8458 (tpp) REVERT: G 116 PHE cc_start: 0.8820 (m-10) cc_final: 0.8585 (m-10) REVERT: G 217 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8678 (mp) REVERT: G 275 ASP cc_start: 0.7960 (t0) cc_final: 0.7634 (t0) REVERT: I 59 MET cc_start: 0.9505 (mmm) cc_final: 0.9030 (mmm) REVERT: I 149 MET cc_start: 0.9112 (mmt) cc_final: 0.8613 (mmm) REVERT: J 48 MET cc_start: 0.9114 (mmp) cc_final: 0.8598 (mmt) REVERT: K 48 MET cc_start: 0.8523 (tpp) cc_final: 0.8298 (tpp) REVERT: K 77 ARG cc_start: 0.8994 (mpp80) cc_final: 0.8561 (mpp80) REVERT: K 100 GLN cc_start: 0.7882 (pp30) cc_final: 0.7585 (pp30) outliers start: 58 outliers final: 46 residues processed: 160 average time/residue: 0.2766 time to fit residues: 68.7989 Evaluate side-chains 156 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 104 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 112 ASP Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain J residue 102 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 199 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17409 Z= 0.293 Angle : 0.581 8.505 23589 Z= 0.295 Chirality : 0.042 0.173 2601 Planarity : 0.004 0.074 3018 Dihedral : 6.514 59.800 2922 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.02 % Allowed : 12.41 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2097 helix: 2.34 (0.28), residues: 339 sheet: 0.22 (0.27), residues: 405 loop : -1.10 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 36 HIS 0.003 0.001 HIS E 101 PHE 0.014 0.001 PHE C 213 TYR 0.010 0.001 TYR D 94 ARG 0.004 0.000 ARG J 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 112 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 275 ASP cc_start: 0.8080 (t0) cc_final: 0.7701 (t0) REVERT: A 314 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9316 (pp) REVERT: B 103 GLU cc_start: 0.9275 (mm-30) cc_final: 0.9030 (mm-30) REVERT: H 80 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7252 (tpp) REVERT: H 85 GLU cc_start: 0.8656 (pm20) cc_final: 0.7835 (pp20) REVERT: L 48 MET cc_start: 0.8781 (tpp) cc_final: 0.8135 (mmm) REVERT: C 217 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 260 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9272 (pp) REVERT: C 275 ASP cc_start: 0.8273 (t0) cc_final: 0.7893 (t0) REVERT: D 17 MET cc_start: 0.8328 (ttp) cc_final: 0.7989 (tmm) REVERT: D 109 ASP cc_start: 0.9394 (m-30) cc_final: 0.9187 (p0) REVERT: D 149 MET cc_start: 0.9060 (mmt) cc_final: 0.8617 (mmm) REVERT: E 48 MET cc_start: 0.8928 (mmm) cc_final: 0.7855 (mtt) REVERT: E 80 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7106 (tpp) REVERT: F 48 MET cc_start: 0.8671 (tpp) cc_final: 0.8439 (tpp) REVERT: G 116 PHE cc_start: 0.8780 (m-10) cc_final: 0.8501 (m-10) REVERT: G 217 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8686 (mp) REVERT: G 275 ASP cc_start: 0.8020 (t0) cc_final: 0.7678 (t0) REVERT: I 17 MET cc_start: 0.8499 (tmm) cc_final: 0.8216 (tmm) REVERT: I 59 MET cc_start: 0.9485 (mmm) cc_final: 0.9044 (mmm) REVERT: I 149 MET cc_start: 0.9066 (mmt) cc_final: 0.8640 (mmm) REVERT: J 48 MET cc_start: 0.8877 (mmp) cc_final: 0.8464 (mmt) REVERT: K 48 MET cc_start: 0.8489 (tpp) cc_final: 0.8260 (tpp) REVERT: K 77 ARG cc_start: 0.9024 (mpp80) cc_final: 0.8574 (mpp80) REVERT: K 100 GLN cc_start: 0.7933 (pp30) cc_final: 0.7606 (pp30) outliers start: 55 outliers final: 42 residues processed: 159 average time/residue: 0.2818 time to fit residues: 69.1798 Evaluate side-chains 157 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain J residue 102 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 98 optimal weight: 0.0170 chunk 18 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17409 Z= 0.368 Angle : 0.630 13.013 23589 Z= 0.322 Chirality : 0.042 0.172 2601 Planarity : 0.005 0.097 3018 Dihedral : 6.559 59.683 2922 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.46 % Allowed : 12.58 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2097 helix: 2.23 (0.28), residues: 339 sheet: 0.05 (0.26), residues: 417 loop : -1.16 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 36 HIS 0.003 0.001 HIS E 101 PHE 0.015 0.002 PHE C 213 TYR 0.011 0.001 TYR I 34 ARG 0.005 0.001 ARG F 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 111 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8586 (mp) REVERT: A 275 ASP cc_start: 0.8059 (t0) cc_final: 0.7660 (t0) REVERT: A 314 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9311 (pp) REVERT: B 89 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9381 (tt) REVERT: H 48 MET cc_start: 0.8452 (mmp) cc_final: 0.7936 (mmt) REVERT: H 80 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: L 48 MET cc_start: 0.8833 (tpp) cc_final: 0.8599 (tpp) REVERT: C 217 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8528 (mp) REVERT: C 260 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9285 (pp) REVERT: C 274 MET cc_start: 0.8769 (tpp) cc_final: 0.8317 (mmm) REVERT: C 275 ASP cc_start: 0.8250 (t0) cc_final: 0.7878 (t0) REVERT: D 17 MET cc_start: 0.8327 (ttp) cc_final: 0.7941 (tmm) REVERT: D 149 MET cc_start: 0.9040 (mmt) cc_final: 0.8595 (mmm) REVERT: E 80 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.6963 (tpp) REVERT: G 116 PHE cc_start: 0.8866 (m-10) cc_final: 0.8598 (m-10) REVERT: G 217 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8692 (mp) REVERT: G 275 ASP cc_start: 0.7976 (t0) cc_final: 0.7639 (t0) REVERT: I 17 MET cc_start: 0.8569 (tmm) cc_final: 0.8304 (tmm) REVERT: I 59 MET cc_start: 0.9501 (mmm) cc_final: 0.9069 (mmm) REVERT: I 149 MET cc_start: 0.9007 (mmt) cc_final: 0.8576 (mmm) REVERT: K 31 SER cc_start: 0.9226 (m) cc_final: 0.9025 (p) REVERT: K 77 ARG cc_start: 0.9063 (mpp80) cc_final: 0.8543 (mpp80) REVERT: K 100 GLN cc_start: 0.8130 (pp30) cc_final: 0.7719 (pp30) outliers start: 63 outliers final: 48 residues processed: 166 average time/residue: 0.2761 time to fit residues: 71.3081 Evaluate side-chains 161 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 105 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain J residue 102 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 HIS C 322 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17409 Z= 0.378 Angle : 0.643 10.725 23589 Z= 0.328 Chirality : 0.043 0.315 2601 Planarity : 0.004 0.058 3018 Dihedral : 6.588 58.762 2922 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.51 % Allowed : 13.07 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2097 helix: 2.17 (0.28), residues: 339 sheet: 0.09 (0.27), residues: 405 loop : -1.27 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 36 HIS 0.004 0.001 HIS D 111 PHE 0.016 0.002 PHE C 213 TYR 0.011 0.001 TYR I 34 ARG 0.007 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 106 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8587 (mp) REVERT: A 275 ASP cc_start: 0.8152 (t0) cc_final: 0.7784 (t0) REVERT: A 314 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9315 (pp) REVERT: B 149 MET cc_start: 0.8994 (mmp) cc_final: 0.8641 (mmp) REVERT: H 48 MET cc_start: 0.8526 (mmp) cc_final: 0.8126 (mmt) REVERT: L 48 MET cc_start: 0.8809 (tpp) cc_final: 0.8562 (tpp) REVERT: C 217 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8532 (mp) REVERT: C 260 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9308 (pp) REVERT: C 274 MET cc_start: 0.8723 (tpp) cc_final: 0.8275 (mmm) REVERT: C 275 ASP cc_start: 0.8359 (t0) cc_final: 0.7986 (t0) REVERT: D 17 MET cc_start: 0.8319 (ttp) cc_final: 0.8065 (tmm) REVERT: D 149 MET cc_start: 0.9053 (mmt) cc_final: 0.8608 (mmm) REVERT: E 48 MET cc_start: 0.9046 (mmm) cc_final: 0.7693 (mtt) REVERT: E 80 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7241 (tpp) REVERT: G 116 PHE cc_start: 0.8889 (m-10) cc_final: 0.8646 (m-10) REVERT: G 217 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8678 (mp) REVERT: G 275 ASP cc_start: 0.7963 (t0) cc_final: 0.7641 (t0) REVERT: I 17 MET cc_start: 0.8594 (tmm) cc_final: 0.8336 (tmm) REVERT: I 59 MET cc_start: 0.9508 (mmm) cc_final: 0.9083 (mmm) REVERT: I 149 MET cc_start: 0.8978 (mmt) cc_final: 0.8554 (mmm) REVERT: J 48 MET cc_start: 0.8514 (mmp) cc_final: 0.8300 (mmt) REVERT: K 48 MET cc_start: 0.8745 (tpp) cc_final: 0.8223 (tpp) REVERT: K 77 ARG cc_start: 0.9069 (mpp80) cc_final: 0.8543 (mpp80) REVERT: K 100 GLN cc_start: 0.8285 (pp30) cc_final: 0.7825 (pp30) outliers start: 64 outliers final: 52 residues processed: 161 average time/residue: 0.3064 time to fit residues: 78.0109 Evaluate side-chains 163 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 105 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 146 ASN Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 67 VAL Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain J residue 102 HIS Chi-restraints excluded: chain K residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 0.0170 chunk 136 optimal weight: 0.0070 chunk 206 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 0.0070 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 HIS C 150 ASN C 190 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 190 ASN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17409 Z= 0.151 Angle : 0.575 9.865 23589 Z= 0.287 Chirality : 0.042 0.166 2601 Planarity : 0.004 0.059 3018 Dihedral : 6.035 58.818 2922 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.14 % Allowed : 14.55 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2097 helix: 2.60 (0.28), residues: 339 sheet: 0.35 (0.27), residues: 405 loop : -1.12 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 36 HIS 0.002 0.001 HIS G 183 PHE 0.012 0.001 PHE C 213 TYR 0.007 0.001 TYR F 87 ARG 0.003 0.000 ARG K 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 275 ASP cc_start: 0.8220 (t0) cc_final: 0.7909 (t0) REVERT: A 314 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9351 (pp) REVERT: B 77 MET cc_start: 0.7532 (mmt) cc_final: 0.7084 (mmt) REVERT: B 149 MET cc_start: 0.9002 (mmp) cc_final: 0.8577 (mmp) REVERT: H 48 MET cc_start: 0.8252 (mmp) cc_final: 0.7906 (mmt) REVERT: L 48 MET cc_start: 0.8707 (tpp) cc_final: 0.8478 (tpp) REVERT: C 217 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8521 (mp) REVERT: C 260 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9236 (pp) REVERT: C 274 MET cc_start: 0.8587 (tpp) cc_final: 0.8106 (mmm) REVERT: C 275 ASP cc_start: 0.8345 (t0) cc_final: 0.8007 (t0) REVERT: D 149 MET cc_start: 0.9077 (mmt) cc_final: 0.8659 (mmm) REVERT: E 48 MET cc_start: 0.8833 (mmm) cc_final: 0.7567 (mtt) REVERT: E 80 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7356 (tpp) REVERT: E 85 GLU cc_start: 0.8674 (pm20) cc_final: 0.8331 (pm20) REVERT: F 18 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8730 (tpp-160) REVERT: F 48 MET cc_start: 0.8755 (tpp) cc_final: 0.8156 (mmm) REVERT: G 116 PHE cc_start: 0.8705 (m-10) cc_final: 0.8359 (m-10) REVERT: G 217 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8719 (mp) REVERT: G 275 ASP cc_start: 0.8069 (t0) cc_final: 0.7733 (t0) REVERT: I 17 MET cc_start: 0.8739 (tmm) cc_final: 0.8516 (tmm) REVERT: I 85 ASP cc_start: 0.9158 (m-30) cc_final: 0.8808 (m-30) REVERT: I 112 ASP cc_start: 0.9231 (m-30) cc_final: 0.8900 (p0) REVERT: I 149 MET cc_start: 0.9078 (mmt) cc_final: 0.8671 (mmm) REVERT: J 48 MET cc_start: 0.8152 (mmp) cc_final: 0.7924 (mmt) REVERT: K 48 MET cc_start: 0.8687 (tpp) cc_final: 0.8107 (tpp) REVERT: K 77 ARG cc_start: 0.9057 (mpp80) cc_final: 0.8501 (mpp80) REVERT: K 100 GLN cc_start: 0.8266 (pp30) cc_final: 0.7815 (pp30) outliers start: 39 outliers final: 28 residues processed: 150 average time/residue: 0.2854 time to fit residues: 66.0023 Evaluate side-chains 145 residues out of total 1821 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 305 CYS Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 100 PHE Chi-restraints excluded: chain J residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 102 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.027588 restraints weight = 124194.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.028629 restraints weight = 63682.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.029338 restraints weight = 41727.403| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17409 Z= 0.270 Angle : 0.593 10.842 23589 Z= 0.297 Chirality : 0.042 0.193 2601 Planarity : 0.004 0.057 3018 Dihedral : 6.120 58.985 2922 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.09 % Allowed : 14.94 % Favored : 82.98 % 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: -0.28 (0.18), residues: 2097 helix: 2.55 (0.28), residues: 339 sheet: 0.31 (0.27), residues: 405 loop : -1.14 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 36 HIS 0.003 0.001 HIS E 101 PHE 0.013 0.001 PHE C 213 TYR 0.008 0.001 TYR D 94 ARG 0.003 0.000 ARG G 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.92 seconds wall clock time: 52 minutes 50.39 seconds (3170.39 seconds total)