Starting phenix.real_space_refine on Sun Mar 17 15:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/03_2024/8bcp_15967.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/03_2024/8bcp_15967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/03_2024/8bcp_15967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/03_2024/8bcp_15967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/03_2024/8bcp_15967.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcp_15967/03_2024/8bcp_15967.pdb" } resolution = 3.88 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= 0.002 sd= 0.014 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 66 5.16 5 C 11412 2.51 5 N 3021 2.21 5 O 3672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "H ASP 33": "OD1" <-> "OD2" Residue "H TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 141": "OD1" <-> "OD2" Residue "H ASP 148": "OD1" <-> "OD2" Residue "H PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 327": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ASP 125": "OD1" <-> "OD2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "I ASP 44": "OD1" <-> "OD2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 141": "OD1" <-> "OD2" Residue "I ASP 148": "OD1" <-> "OD2" Residue "I PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 306": "OE1" <-> "OE2" Residue "I ASP 327": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18171 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "D" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1243 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "H" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "B" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1243 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "E" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "F" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1243 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Time building chain proxies: 9.37, per 1000 atoms: 0.52 Number of scatterers: 18171 At special positions: 0 Unit cell: (154.014, 163.471, 104.027, 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 66 16.00 O 3672 8.00 N 3021 7.00 C 11412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 33 sheets defined 15.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 85 through 103 removed outlier: 3.656A pdb=" N GLN C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'H' and resid 5 through 7 No H-bonds generated for 'chain 'H' and resid 5 through 7' Processing helix chain 'H' and resid 91 through 100 removed outlier: 3.600A pdb=" N TRP H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 275 through 287 Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.634A pdb=" N GLN A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 91 through 100 removed outlier: 3.766A pdb=" N TRP G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'G' and resid 192 through 200 Processing helix chain 'G' and resid 275 through 287 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 85 through 103 removed outlier: 3.545A pdb=" N GLN E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 18 Processing helix chain 'F' and resid 85 through 103 Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 91 through 100 removed outlier: 3.774A pdb=" N TRP I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 190 Processing helix chain 'I' and resid 192 through 200 Processing helix chain 'I' and resid 275 through 287 Processing helix chain 'I' and resid 358 through 369 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.622A pdb=" N SER C 36 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 58 through 62 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 73 current: chain 'C' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 144 through 152 current: chain 'D' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 53 current: chain 'D' and resid 68 through 79 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 79 current: chain 'D' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 144 through 152 current: chain 'A' and resid 70 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 73 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'B' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 53 current: chain 'B' and resid 68 through 79 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 79 current: chain 'B' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 152 current: chain 'E' and resid 70 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 70 through 73 current: chain 'E' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 152 current: chain 'F' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 53 current: chain 'F' and resid 68 through 79 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 79 current: chain 'F' and resid 143 through 152 Processing sheet with id=AA3, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AA4, first strand: chain 'D' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'H' and resid 25 through 28 removed outlier: 4.362A pdb=" N ILE H 11 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE H 136 " --> pdb=" O ILE H 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 75 current: chain 'H' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 119 through 122 current: chain 'H' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 166 through 173 current: chain 'H' and resid 220 through 222 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 220 through 222 current: chain 'H' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 260 through 268 current: chain 'H' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 307 through 319 current: chain 'H' and resid 331 through 337 Processing sheet with id=AA7, first strand: chain 'H' and resid 43 through 46 removed outlier: 3.843A pdb=" N ILE H 45 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 59 " --> pdb=" O ILE H 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'H' and resid 238 through 240 removed outlier: 3.642A pdb=" N GLY H 253 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 378 through 382 removed outlier: 3.514A pdb=" N ALA H 378 " --> pdb=" O THR H 403 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR H 403 " --> pdb=" O ALA H 378 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR H 380 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 389 through 390 removed outlier: 3.893A pdb=" N LEU H 390 " --> pdb=" O THR H 459 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS H 456 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 445 " --> pdb=" O THR H 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 395 through 396 removed outlier: 3.660A pdb=" N LEU H 430 " --> pdb=" O LEU H 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.552A pdb=" N SER A 36 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AB6, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB7, first strand: chain 'G' and resid 9 through 14 removed outlier: 4.350A pdb=" N ILE G 11 " --> pdb=" O ILE G 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 28 current: chain 'G' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 75 current: chain 'G' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 119 through 122 current: chain 'G' and resid 143 through 158 removed outlier: 5.895A pdb=" N ILE G 152 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN G 172 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN G 158 " --> pdb=" O ARG G 166 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG G 166 " --> pdb=" O ASN G 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 173 current: chain 'G' and resid 220 through 222 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 220 through 222 current: chain 'G' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 260 through 268 current: chain 'G' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 307 through 319 current: chain 'G' and resid 331 through 337 Processing sheet with id=AB8, first strand: chain 'G' and resid 43 through 46 removed outlier: 3.828A pdb=" N ILE G 45 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 59 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 79 through 80 Processing sheet with id=AC1, first strand: chain 'G' and resid 238 through 240 removed outlier: 3.847A pdb=" N GLY G 253 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 378 through 382 removed outlier: 3.539A pdb=" N ALA G 378 " --> pdb=" O THR G 403 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 403 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR G 380 " --> pdb=" O GLU G 401 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 389 through 390 removed outlier: 3.711A pdb=" N LEU G 390 " --> pdb=" O THR G 459 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS G 456 " --> pdb=" O VAL G 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 395 through 396 removed outlier: 3.578A pdb=" N LEU G 430 " --> pdb=" O LEU G 396 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 35 through 36 removed outlier: 7.246A pdb=" N SER E 36 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AC7, first strand: chain 'F' and resid 108 through 111 Processing sheet with id=AC8, first strand: chain 'I' and resid 9 through 14 removed outlier: 4.373A pdb=" N ILE I 11 " --> pdb=" O ILE I 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 28 current: chain 'I' and resid 68 through 75 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 75 current: chain 'I' and resid 143 through 158 removed outlier: 5.723A pdb=" N ILE I 152 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN I 172 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN I 158 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG I 166 " --> pdb=" O ASN I 158 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 173 current: chain 'I' and resid 220 through 222 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 220 through 222 current: chain 'I' and resid 260 through 268 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 260 through 268 current: chain 'I' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 307 through 319 current: chain 'I' and resid 331 through 337 Processing sheet with id=AC9, first strand: chain 'I' and resid 43 through 46 removed outlier: 3.931A pdb=" N ILE I 45 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS I 59 " --> pdb=" O ILE I 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 79 through 80 Processing sheet with id=AD2, first strand: chain 'I' and resid 111 through 114 Processing sheet with id=AD3, first strand: chain 'I' and resid 238 through 240 removed outlier: 3.605A pdb=" N GLY I 253 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 378 through 382 removed outlier: 3.512A pdb=" N ALA I 378 " --> pdb=" O THR I 403 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR I 380 " --> pdb=" O GLU I 401 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 389 through 390 removed outlier: 3.723A pdb=" N LEU I 390 " --> pdb=" O THR I 459 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS I 456 " --> pdb=" O VAL I 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 395 through 396 removed outlier: 3.673A pdb=" N LEU I 430 " --> pdb=" O LEU I 396 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1083 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6039 1.34 - 1.46: 3176 1.46 - 1.57: 9163 1.57 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 18501 Sorted by residual: bond pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" C GLU F 47 " pdb=" N PHE F 48 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.59e-02 3.96e+03 2.26e+00 bond pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 1.536 1.562 -0.026 2.08e-02 2.31e+03 1.59e+00 bond pdb=" CA GLU G 302 " pdb=" CB GLU G 302 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.50e-02 4.44e+03 1.41e+00 bond pdb=" CB ASN B 115 " pdb=" CG ASN B 115 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.18e+00 ... (remaining 18496 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.39: 348 105.39 - 112.55: 9763 112.55 - 119.71: 5967 119.71 - 126.87: 8897 126.87 - 134.03: 186 Bond angle restraints: 25161 Sorted by residual: angle pdb=" CA GLU B 44 " pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " ideal model delta sigma weight residual 114.10 120.42 -6.32 2.00e+00 2.50e-01 1.00e+01 angle pdb=" N GLY D 60 " pdb=" CA GLY D 60 " pdb=" C GLY D 60 " ideal model delta sigma weight residual 110.87 115.35 -4.48 1.54e+00 4.22e-01 8.45e+00 angle pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " pdb=" CD GLU E 91 " ideal model delta sigma weight residual 112.60 117.51 -4.91 1.70e+00 3.46e-01 8.34e+00 angle pdb=" CA GLU E 91 " pdb=" CB GLU E 91 " pdb=" CG GLU E 91 " ideal model delta sigma weight residual 114.10 119.84 -5.74 2.00e+00 2.50e-01 8.23e+00 angle pdb=" CA GLU A 58 " pdb=" CB GLU A 58 " pdb=" CG GLU A 58 " ideal model delta sigma weight residual 114.10 119.66 -5.56 2.00e+00 2.50e-01 7.73e+00 ... (remaining 25156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9566 17.89 - 35.79: 1198 35.79 - 53.68: 291 53.68 - 71.57: 59 71.57 - 89.47: 22 Dihedral angle restraints: 11136 sinusoidal: 4365 harmonic: 6771 Sorted by residual: dihedral pdb=" CA ASP I 141 " pdb=" CB ASP I 141 " pdb=" CG ASP I 141 " pdb=" OD1 ASP I 141 " ideal model delta sinusoidal sigma weight residual -30.00 -88.83 58.83 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ILE B 45 " pdb=" C ILE B 45 " pdb=" N ARG B 46 " pdb=" CA ARG B 46 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU G 107 " pdb=" CG GLU G 107 " pdb=" CD GLU G 107 " pdb=" OE1 GLU G 107 " ideal model delta sinusoidal sigma weight residual 0.00 89.47 -89.47 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 11133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1832 0.031 - 0.061: 658 0.061 - 0.092: 220 0.092 - 0.122: 193 0.122 - 0.153: 16 Chirality restraints: 2919 Sorted by residual: chirality pdb=" CA ASN B 115 " pdb=" N ASN B 115 " pdb=" C ASN B 115 " pdb=" CB ASN B 115 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA PRO F 64 " pdb=" N PRO F 64 " pdb=" C PRO F 64 " pdb=" CB PRO F 64 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA PRO B 64 " pdb=" N PRO B 64 " pdb=" C PRO B 64 " pdb=" CB PRO B 64 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2916 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 115 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C ASN B 115 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 115 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 116 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 58 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLU B 58 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 58 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 63 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO F 64 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " 0.026 5.00e-02 4.00e+02 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 692 2.70 - 3.25: 17681 3.25 - 3.80: 27836 3.80 - 4.35: 34983 4.35 - 4.90: 60889 Nonbonded interactions: 142081 Sorted by model distance: nonbonded pdb=" OG SER E 36 " pdb=" OH TYR E 50 " model vdw 2.151 2.440 nonbonded pdb=" OD1 ASN B 115 " pdb=" OG SER B 117 " model vdw 2.180 2.440 nonbonded pdb=" OD1 ASN F 115 " pdb=" OG SER F 117 " model vdw 2.200 2.440 nonbonded pdb=" O THR D 99 " pdb=" OG1 THR D 103 " model vdw 2.214 2.440 nonbonded pdb=" O THR B 99 " pdb=" OG1 THR B 103 " model vdw 2.215 2.440 ... (remaining 142076 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' and resid 1 through 156) selection = chain 'B' selection = (chain 'C' and resid 1 through 156) selection = chain 'D' selection = (chain 'E' and resid 1 through 156) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.820 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 45.290 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 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 0.047 18501 Z= 0.176 Angle : 0.528 7.063 25161 Z= 0.286 Chirality : 0.043 0.153 2919 Planarity : 0.004 0.057 3264 Dihedral : 17.057 89.469 6792 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 0.30 % Allowed : 28.00 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.67 (0.17), residues: 2319 helix: 1.70 (0.29), residues: 318 sheet: -0.11 (0.20), residues: 780 loop : -1.27 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 144 HIS 0.004 0.001 HIS H 318 PHE 0.032 0.001 PHE I 231 TYR 0.019 0.001 TYR H 303 ARG 0.003 0.000 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 571 time to evaluate : 2.087 Fit side-chains revert: symmetry clash REVERT: C 103 THR cc_start: 0.4594 (p) cc_final: 0.4340 (p) REVERT: D 41 LYS cc_start: 0.6069 (mttm) cc_final: 0.5628 (tptp) REVERT: D 122 GLU cc_start: 0.6353 (pt0) cc_final: 0.6045 (pm20) REVERT: D 156 ARG cc_start: 0.4413 (pmt-80) cc_final: 0.3203 (tpm170) REVERT: H 1 MET cc_start: 0.6133 (ttp) cc_final: 0.5834 (ttp) REVERT: H 139 LEU cc_start: 0.7109 (tt) cc_final: 0.6725 (tt) REVERT: H 347 ASP cc_start: 0.5862 (p0) cc_final: 0.5446 (t0) REVERT: A 1 MET cc_start: 0.5695 (mpp) cc_final: 0.5099 (mmt) REVERT: A 29 ASN cc_start: 0.7357 (m110) cc_final: 0.6861 (m110) REVERT: A 79 TYR cc_start: 0.5359 (m-80) cc_final: 0.5121 (m-10) REVERT: A 114 PRO cc_start: 0.8092 (Cg_exo) cc_final: 0.7888 (Cg_endo) REVERT: B 1 MET cc_start: 0.2613 (pmm) cc_final: 0.0679 (mmm) REVERT: B 86 ILE cc_start: 0.6285 (tt) cc_final: 0.5630 (tt) REVERT: B 132 SER cc_start: 0.4907 (t) cc_final: 0.4283 (m) REVERT: G 189 ILE cc_start: 0.5985 (mm) cc_final: 0.5693 (mm) REVERT: F 83 LYS cc_start: 0.6358 (mtmm) cc_final: 0.6058 (mttt) REVERT: F 101 ILE cc_start: 0.7851 (mm) cc_final: 0.7549 (mm) REVERT: I 129 HIS cc_start: 0.4165 (m-70) cc_final: 0.3686 (m-70) outliers start: 6 outliers final: 1 residues processed: 574 average time/residue: 0.2976 time to fit residues: 254.7673 Evaluate side-chains 366 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 365 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 86 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 178 optimal weight: 40.0000 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN C 153 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN H 182 GLN H 206 ASN H 316 GLN H 318 HIS H 386 ASN A 54 HIS A 106 ASN B 54 HIS B 67 GLN G 38 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 386 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 ASN I 386 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 18501 Z= 0.421 Angle : 0.872 14.144 25161 Z= 0.458 Chirality : 0.055 0.310 2919 Planarity : 0.007 0.089 3264 Dihedral : 5.480 39.075 2513 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.43 % Favored : 94.44 % Rotamer: Outliers : 9.04 % Allowed : 24.69 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2319 helix: 0.14 (0.25), residues: 342 sheet: -0.43 (0.20), residues: 729 loop : -1.75 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP H 144 HIS 0.008 0.002 HIS F 3 PHE 0.039 0.003 PHE I 12 TYR 0.039 0.003 TYR F 62 ARG 0.012 0.001 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 418 time to evaluate : 2.242 Fit side-chains REVERT: C 70 MET cc_start: 0.7491 (tmm) cc_final: 0.7229 (ttp) REVERT: C 72 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7676 (tt) REVERT: D 59 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7724 (t) REVERT: D 122 GLU cc_start: 0.7340 (pt0) cc_final: 0.6991 (pm20) REVERT: D 156 ARG cc_start: 0.5960 (pmt-80) cc_final: 0.3825 (tpm170) REVERT: H 120 MET cc_start: 0.7908 (pmm) cc_final: 0.7358 (pmm) REVERT: H 142 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7208 (mttt) REVERT: H 184 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7420 (p90) REVERT: H 197 MET cc_start: 0.7572 (mmm) cc_final: 0.7360 (ttm) REVERT: H 278 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6567 (mm-30) REVERT: H 285 LYS cc_start: 0.7307 (ttpp) cc_final: 0.6992 (mmtt) REVERT: H 324 ILE cc_start: 0.8171 (tt) cc_final: 0.7855 (tt) REVERT: H 398 MET cc_start: 0.3000 (pmm) cc_final: 0.1751 (ttm) REVERT: A 1 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7396 (pmm) REVERT: A 29 ASN cc_start: 0.7963 (m110) cc_final: 0.7726 (m110) REVERT: A 70 MET cc_start: 0.7533 (ttm) cc_final: 0.7019 (ttm) REVERT: A 114 PRO cc_start: 0.8109 (Cg_exo) cc_final: 0.7816 (Cg_endo) REVERT: A 156 ARG cc_start: 0.7307 (tmm-80) cc_final: 0.7069 (ptm160) REVERT: B 4 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6245 (ptm-80) REVERT: B 18 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7276 (mt0) REVERT: B 69 TRP cc_start: 0.8734 (m100) cc_final: 0.7873 (m100) REVERT: B 80 ASP cc_start: 0.6154 (t0) cc_final: 0.5718 (t0) REVERT: G 4 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: G 38 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: G 100 SER cc_start: 0.8855 (t) cc_final: 0.8494 (p) REVERT: G 187 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6531 (t0) REVERT: G 247 ARG cc_start: 0.8127 (mpp80) cc_final: 0.7872 (mtt90) REVERT: G 255 PHE cc_start: 0.7326 (m-10) cc_final: 0.7095 (m-80) REVERT: E 26 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6172 (mm-30) REVERT: E 101 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6928 (tt) REVERT: F 11 MET cc_start: 0.7299 (tpp) cc_final: 0.6952 (tpp) REVERT: F 58 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: F 70 MET cc_start: 0.6940 (tpp) cc_final: 0.6673 (tpp) REVERT: I 120 MET cc_start: 0.7422 (ptm) cc_final: 0.7162 (ptt) REVERT: I 180 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6967 (t0) REVERT: I 203 TYR cc_start: 0.8454 (m-80) cc_final: 0.8224 (m-80) outliers start: 183 outliers final: 75 residues processed: 562 average time/residue: 0.2966 time to fit residues: 251.9259 Evaluate side-chains 398 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 309 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 184 PHE Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 321 ILE Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain H residue 461 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 278 GLU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain G residue 455 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 357 TYR Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 388 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 224 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN D 87 GLN H 38 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 89 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN F 89 GLN I 4 GLN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 219 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18501 Z= 0.189 Angle : 0.537 7.090 25161 Z= 0.282 Chirality : 0.044 0.232 2919 Planarity : 0.004 0.052 3264 Dihedral : 4.461 37.328 2513 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.41 % Rotamer: Outliers : 5.28 % Allowed : 28.20 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2319 helix: 1.20 (0.27), residues: 330 sheet: -0.43 (0.19), residues: 759 loop : -1.40 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.005 0.001 HIS I 318 PHE 0.017 0.001 PHE G 123 TYR 0.015 0.001 TYR H 303 ARG 0.005 0.001 ARG G 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 317 time to evaluate : 2.150 Fit side-chains REVERT: C 11 MET cc_start: 0.7161 (ttm) cc_final: 0.6917 (tpp) REVERT: D 25 ASP cc_start: 0.8062 (m-30) cc_final: 0.7850 (m-30) REVERT: D 122 GLU cc_start: 0.7323 (pt0) cc_final: 0.6851 (pm20) REVERT: D 143 LEU cc_start: 0.9225 (pt) cc_final: 0.9020 (pp) REVERT: D 156 ARG cc_start: 0.5935 (pmt-80) cc_final: 0.3664 (tpm170) REVERT: H 63 ASP cc_start: 0.7009 (p0) cc_final: 0.6248 (m-30) REVERT: H 120 MET cc_start: 0.7846 (pmm) cc_final: 0.7587 (ptp) REVERT: H 142 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7125 (mttt) REVERT: A 29 ASN cc_start: 0.7961 (m110) cc_final: 0.7699 (m-40) REVERT: A 77 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7865 (pp) REVERT: A 113 LYS cc_start: 0.7649 (tttt) cc_final: 0.7189 (mmtt) REVERT: B 3 HIS cc_start: 0.5873 (OUTLIER) cc_final: 0.5665 (m90) REVERT: B 4 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6190 (ptm-80) REVERT: B 69 TRP cc_start: 0.8730 (m100) cc_final: 0.7884 (m100) REVERT: B 80 ASP cc_start: 0.6366 (t0) cc_final: 0.5990 (t0) REVERT: B 91 GLU cc_start: 0.6204 (OUTLIER) cc_final: 0.5376 (tm-30) REVERT: B 113 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5980 (mttm) REVERT: B 126 MET cc_start: 0.7826 (mmt) cc_final: 0.7388 (mmt) REVERT: G 234 ASN cc_start: 0.8219 (t0) cc_final: 0.7919 (t0) REVERT: G 247 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7792 (mtt90) REVERT: G 287 LEU cc_start: 0.8267 (tp) cc_final: 0.7851 (mt) REVERT: G 370 ASP cc_start: 0.8412 (t70) cc_final: 0.7941 (t0) REVERT: F 4 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7495 (mtp-110) REVERT: F 91 GLU cc_start: 0.6704 (tm-30) cc_final: 0.6218 (tm-30) REVERT: F 101 ILE cc_start: 0.8204 (mm) cc_final: 0.8004 (mm) REVERT: I 180 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7085 (t0) outliers start: 107 outliers final: 57 residues processed: 394 average time/residue: 0.2652 time to fit residues: 164.0629 Evaluate side-chains 356 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 291 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 306 GLU Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 247 ARG Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 149 SER Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 214 LYS Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 430 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 HIS ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN I 4 GLN I 62 ASN ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18501 Z= 0.247 Angle : 0.546 11.230 25161 Z= 0.287 Chirality : 0.045 0.211 2919 Planarity : 0.004 0.049 3264 Dihedral : 4.328 39.207 2513 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.23 % Favored : 95.64 % Rotamer: Outliers : 6.91 % Allowed : 26.57 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2319 helix: 1.38 (0.27), residues: 333 sheet: -0.55 (0.19), residues: 822 loop : -1.38 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 144 HIS 0.006 0.001 HIS I 318 PHE 0.014 0.001 PHE G 123 TYR 0.017 0.002 TYR C 152 ARG 0.005 0.000 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 307 time to evaluate : 2.159 Fit side-chains REVERT: D 18 GLN cc_start: 0.7556 (mt0) cc_final: 0.7280 (mt0) REVERT: D 40 TYR cc_start: 0.5732 (m-80) cc_final: 0.5460 (m-80) REVERT: D 70 MET cc_start: 0.7759 (mmt) cc_final: 0.7517 (mmm) REVERT: D 156 ARG cc_start: 0.6346 (pmt-80) cc_final: 0.3809 (tpm170) REVERT: H 2 SER cc_start: 0.7611 (p) cc_final: 0.7165 (m) REVERT: H 63 ASP cc_start: 0.6991 (p0) cc_final: 0.6278 (m-30) REVERT: H 120 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8148 (ptp) REVERT: H 142 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7289 (mttt) REVERT: A 1 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: A 77 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7888 (pp) REVERT: A 91 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 113 LYS cc_start: 0.7503 (tttt) cc_final: 0.7030 (mmtt) REVERT: B 4 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6047 (ptm-80) REVERT: B 45 ILE cc_start: 0.6705 (mm) cc_final: 0.6237 (mm) REVERT: B 69 TRP cc_start: 0.8920 (m100) cc_final: 0.8052 (m100) REVERT: B 80 ASP cc_start: 0.7059 (t0) cc_final: 0.6656 (t0) REVERT: B 113 LYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5566 (mttm) REVERT: G 63 ASP cc_start: 0.6472 (p0) cc_final: 0.5713 (m-30) REVERT: G 247 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7857 (mtp180) REVERT: G 283 LEU cc_start: 0.8245 (mt) cc_final: 0.8000 (mt) REVERT: E 16 SER cc_start: 0.7500 (m) cc_final: 0.7056 (t) REVERT: F 4 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7517 (mtp-110) REVERT: F 58 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: F 73 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7880 (tm-30) REVERT: I 32 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6565 (m-30) outliers start: 140 outliers final: 94 residues processed: 407 average time/residue: 0.2629 time to fit residues: 169.7625 Evaluate side-chains 386 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 283 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 326 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 347 ASP Chi-restraints excluded: chain H residue 351 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 247 ARG Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 4 ARG Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 32 ASP Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 180 ASP Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 224 ILE Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 388 THR Chi-restraints excluded: chain I residue 403 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 126 ASN H 151 GLN H 182 GLN B 89 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 ASN ** I 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.9794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18501 Z= 0.425 Angle : 0.712 8.260 25161 Z= 0.374 Chirality : 0.050 0.204 2919 Planarity : 0.005 0.061 3264 Dihedral : 5.182 47.908 2513 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 8.89 % Allowed : 25.23 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2319 helix: 0.72 (0.25), residues: 348 sheet: -0.86 (0.18), residues: 804 loop : -1.58 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 144 HIS 0.007 0.002 HIS I 318 PHE 0.032 0.002 PHE C 119 TYR 0.035 0.002 TYR H 303 ARG 0.008 0.001 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 299 time to evaluate : 2.224 Fit side-chains REVERT: C 158 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7748 (p) REVERT: D 14 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8109 (ttt180) REVERT: D 25 ASP cc_start: 0.8579 (m-30) cc_final: 0.8303 (m-30) REVERT: D 108 GLU cc_start: 0.6752 (pt0) cc_final: 0.6417 (pt0) REVERT: D 126 MET cc_start: 0.8222 (tpt) cc_final: 0.7855 (tpt) REVERT: H 23 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8515 (t) REVERT: H 120 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8415 (ptp) REVERT: H 142 LYS cc_start: 0.7869 (mmmt) cc_final: 0.7405 (mttp) REVERT: H 210 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8880 (pt) REVERT: H 370 ASP cc_start: 0.7636 (t0) cc_final: 0.7267 (t70) REVERT: A 11 MET cc_start: 0.8115 (tpt) cc_final: 0.7737 (tpt) REVERT: A 86 ILE cc_start: 0.8286 (mm) cc_final: 0.7876 (mt) REVERT: A 91 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6590 (tm-30) REVERT: B 4 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6552 (ptm-80) REVERT: B 13 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7472 (t0) REVERT: B 18 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: B 69 TRP cc_start: 0.9033 (m100) cc_final: 0.8139 (m100) REVERT: B 80 ASP cc_start: 0.7297 (t0) cc_final: 0.6978 (t0) REVERT: B 89 GLN cc_start: 0.7211 (mt0) cc_final: 0.6885 (mt0) REVERT: B 96 ASP cc_start: 0.7699 (t70) cc_final: 0.7029 (m-30) REVERT: B 113 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.5639 (mttm) REVERT: G 306 GLU cc_start: 0.7521 (mp0) cc_final: 0.7252 (mp0) REVERT: E 4 ARG cc_start: 0.7125 (tpp80) cc_final: 0.6850 (ttp80) REVERT: E 6 SER cc_start: 0.7390 (m) cc_final: 0.7124 (m) REVERT: E 11 MET cc_start: 0.7470 (tpp) cc_final: 0.7229 (tpp) REVERT: F 58 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: F 59 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8395 (m) REVERT: F 91 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7020 (tm-30) REVERT: F 93 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8468 (mp) REVERT: I 44 ASP cc_start: 0.7644 (t0) cc_final: 0.7443 (t0) outliers start: 180 outliers final: 113 residues processed: 445 average time/residue: 0.2635 time to fit residues: 183.3815 Evaluate side-chains 395 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 271 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 342 ASP Chi-restraints excluded: chain H residue 440 VAL Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 3 HIS Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 13 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 265 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 388 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 150 CYS Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 388 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 450 SER Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 40.0000 chunk 115 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 182 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.9900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18501 Z= 0.208 Angle : 0.544 7.469 25161 Z= 0.284 Chirality : 0.045 0.159 2919 Planarity : 0.004 0.048 3264 Dihedral : 4.620 49.567 2513 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 5.78 % Allowed : 28.00 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2319 helix: 1.29 (0.27), residues: 333 sheet: -0.74 (0.18), residues: 819 loop : -1.46 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 144 HIS 0.006 0.001 HIS I 318 PHE 0.017 0.001 PHE I 231 TYR 0.015 0.001 TYR G 280 ARG 0.006 0.000 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 305 time to evaluate : 1.878 Fit side-chains REVERT: C 62 TYR cc_start: 0.8730 (m-80) cc_final: 0.8388 (m-80) REVERT: D 14 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8099 (ttt180) REVERT: D 25 ASP cc_start: 0.8577 (m-30) cc_final: 0.8314 (m-30) REVERT: D 70 MET cc_start: 0.8047 (mmt) cc_final: 0.7685 (mmm) REVERT: D 91 GLU cc_start: 0.7975 (tp30) cc_final: 0.7588 (tm-30) REVERT: H 120 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8444 (ptp) REVERT: H 141 ASP cc_start: 0.6358 (t70) cc_final: 0.6109 (t70) REVERT: H 142 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7508 (mttp) REVERT: H 370 ASP cc_start: 0.7261 (t0) cc_final: 0.6791 (t70) REVERT: A 86 ILE cc_start: 0.8217 (mm) cc_final: 0.7761 (mt) REVERT: A 91 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6363 (tm-30) REVERT: B 4 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6377 (ptm-80) REVERT: B 18 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7104 (mt0) REVERT: B 69 TRP cc_start: 0.9062 (m100) cc_final: 0.8112 (m100) REVERT: B 80 ASP cc_start: 0.7277 (t0) cc_final: 0.6925 (t0) REVERT: B 89 GLN cc_start: 0.7216 (mt0) cc_final: 0.6772 (mt0) REVERT: B 96 ASP cc_start: 0.7326 (t70) cc_final: 0.6848 (m-30) REVERT: B 113 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5920 (mttm) REVERT: G 261 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8968 (tt) REVERT: G 277 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7751 (mmm) REVERT: E 4 ARG cc_start: 0.6928 (tpp80) cc_final: 0.6711 (ttp80) REVERT: E 91 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6609 (tm-30) REVERT: F 59 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8306 (m) REVERT: F 70 MET cc_start: 0.6940 (tpp) cc_final: 0.6678 (mmt) REVERT: F 73 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7499 (tm-30) REVERT: F 93 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8492 (mp) REVERT: I 44 ASP cc_start: 0.7635 (t0) cc_final: 0.7427 (t0) REVERT: I 49 GLU cc_start: 0.6276 (tp30) cc_final: 0.5835 (tt0) REVERT: I 139 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8344 (tp) REVERT: I 153 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7906 (t0) REVERT: I 210 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8842 (pt) outliers start: 117 outliers final: 76 residues processed: 391 average time/residue: 0.2573 time to fit residues: 158.8819 Evaluate side-chains 373 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 286 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 153 ASN Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 124 optimal weight: 0.0570 chunk 185 optimal weight: 0.2980 chunk 123 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 182 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 ASN ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 1.0055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18501 Z= 0.254 Angle : 0.555 7.577 25161 Z= 0.288 Chirality : 0.045 0.171 2919 Planarity : 0.004 0.048 3264 Dihedral : 4.552 51.116 2513 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.44 % Favored : 95.47 % Rotamer: Outliers : 5.78 % Allowed : 28.10 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2319 helix: 1.22 (0.27), residues: 348 sheet: -0.71 (0.19), residues: 819 loop : -1.47 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 70 HIS 0.005 0.001 HIS I 318 PHE 0.014 0.001 PHE I 231 TYR 0.021 0.002 TYR G 303 ARG 0.004 0.000 ARG F 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 299 time to evaluate : 2.235 Fit side-chains revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8781 (m-80) cc_final: 0.8444 (m-80) REVERT: D 14 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8114 (ttt180) REVERT: D 25 ASP cc_start: 0.8598 (m-30) cc_final: 0.8342 (m-30) REVERT: D 91 GLU cc_start: 0.8015 (tp30) cc_final: 0.7634 (tm-30) REVERT: H 120 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8522 (ptp) REVERT: H 136 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8546 (mt) REVERT: H 141 ASP cc_start: 0.6381 (t70) cc_final: 0.6148 (t70) REVERT: H 142 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7526 (mttp) REVERT: H 370 ASP cc_start: 0.7383 (t0) cc_final: 0.7013 (t70) REVERT: A 86 ILE cc_start: 0.8206 (mm) cc_final: 0.7765 (mt) REVERT: A 91 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6274 (tm-30) REVERT: B 4 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6390 (ptm-80) REVERT: B 18 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: B 70 MET cc_start: 0.7014 (mmt) cc_final: 0.6681 (mmm) REVERT: B 80 ASP cc_start: 0.7380 (t0) cc_final: 0.7005 (t0) REVERT: B 89 GLN cc_start: 0.7260 (mt0) cc_final: 0.6797 (mt0) REVERT: B 96 ASP cc_start: 0.7726 (t70) cc_final: 0.6955 (m-30) REVERT: B 113 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5806 (mttm) REVERT: G 261 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9003 (tt) REVERT: G 277 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7873 (mmm) REVERT: G 286 THR cc_start: 0.7683 (t) cc_final: 0.7116 (p) REVERT: G 306 GLU cc_start: 0.7066 (mp0) cc_final: 0.6663 (mm-30) REVERT: G 348 GLU cc_start: 0.7414 (mp0) cc_final: 0.7057 (mp0) REVERT: E 91 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6573 (tm-30) REVERT: F 58 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: F 59 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8206 (t) REVERT: F 93 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8553 (mp) REVERT: I 44 ASP cc_start: 0.7553 (t0) cc_final: 0.7343 (t0) REVERT: I 49 GLU cc_start: 0.6345 (tp30) cc_final: 0.5883 (tt0) REVERT: I 210 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8858 (pt) outliers start: 117 outliers final: 89 residues processed: 392 average time/residue: 0.2576 time to fit residues: 159.7992 Evaluate side-chains 389 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 289 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 319 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 327 ASP Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.0050 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 0.0270 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.7856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 182 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 1.0154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18501 Z= 0.198 Angle : 0.528 7.251 25161 Z= 0.273 Chirality : 0.044 0.156 2919 Planarity : 0.003 0.048 3264 Dihedral : 4.399 52.899 2513 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.38 % Rotamer: Outliers : 5.63 % Allowed : 28.40 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2319 helix: 1.31 (0.27), residues: 348 sheet: -0.69 (0.18), residues: 822 loop : -1.42 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 70 HIS 0.006 0.001 HIS I 318 PHE 0.015 0.001 PHE I 231 TYR 0.019 0.001 TYR G 303 ARG 0.006 0.000 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 315 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8741 (m-80) cc_final: 0.8460 (m-80) REVERT: D 14 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8129 (ttt180) REVERT: D 25 ASP cc_start: 0.8602 (m-30) cc_final: 0.8366 (m-30) REVERT: D 70 MET cc_start: 0.8196 (mmt) cc_final: 0.7866 (mmm) REVERT: D 91 GLU cc_start: 0.8028 (tp30) cc_final: 0.7579 (tm-30) REVERT: H 120 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8571 (ptp) REVERT: H 136 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8531 (mt) REVERT: H 141 ASP cc_start: 0.6245 (t70) cc_final: 0.6021 (t70) REVERT: H 142 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7494 (mttp) REVERT: H 210 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8976 (pt) REVERT: H 269 LEU cc_start: 0.8742 (mt) cc_final: 0.8047 (mt) REVERT: H 370 ASP cc_start: 0.7298 (t0) cc_final: 0.6871 (t70) REVERT: A 48 PHE cc_start: 0.8853 (m-80) cc_final: 0.8587 (m-80) REVERT: A 86 ILE cc_start: 0.8192 (mm) cc_final: 0.7748 (mt) REVERT: A 91 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6106 (tm-30) REVERT: B 4 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6364 (ptm-80) REVERT: B 18 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: B 80 ASP cc_start: 0.7416 (t0) cc_final: 0.7015 (t0) REVERT: B 89 GLN cc_start: 0.7250 (mt0) cc_final: 0.6770 (mt0) REVERT: B 113 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5900 (mttm) REVERT: G 261 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8884 (tt) REVERT: G 277 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: G 286 THR cc_start: 0.7540 (t) cc_final: 0.6944 (p) REVERT: G 306 GLU cc_start: 0.7045 (mp0) cc_final: 0.6634 (mm-30) REVERT: G 348 GLU cc_start: 0.7356 (mp0) cc_final: 0.6945 (mp0) REVERT: E 91 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6574 (tm-30) REVERT: F 91 GLU cc_start: 0.7140 (tm-30) cc_final: 0.6879 (tm-30) REVERT: I 29 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7639 (pt) REVERT: I 44 ASP cc_start: 0.7548 (t0) cc_final: 0.7335 (t0) REVERT: I 49 GLU cc_start: 0.6857 (tp30) cc_final: 0.6336 (tt0) REVERT: I 139 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8397 (tp) outliers start: 114 outliers final: 88 residues processed: 399 average time/residue: 0.2584 time to fit residues: 163.8597 Evaluate side-chains 410 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 312 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 450 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 388 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 0.3980 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 0.0770 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** G 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 1.0245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18501 Z= 0.202 Angle : 0.528 7.306 25161 Z= 0.274 Chirality : 0.044 0.147 2919 Planarity : 0.003 0.048 3264 Dihedral : 4.338 54.492 2513 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 5.38 % Allowed : 29.23 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2319 helix: 1.42 (0.27), residues: 345 sheet: -0.75 (0.18), residues: 825 loop : -1.40 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 70 HIS 0.006 0.001 HIS I 318 PHE 0.014 0.001 PHE I 231 TYR 0.015 0.001 TYR G 280 ARG 0.005 0.000 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 307 time to evaluate : 2.012 Fit side-chains revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8755 (m-80) cc_final: 0.8434 (m-80) REVERT: D 14 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8109 (ttt180) REVERT: D 25 ASP cc_start: 0.8571 (m-30) cc_final: 0.8335 (m-30) REVERT: D 70 MET cc_start: 0.8197 (mmt) cc_final: 0.7880 (mmm) REVERT: D 91 GLU cc_start: 0.8087 (tp30) cc_final: 0.7658 (tm-30) REVERT: H 136 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8560 (mt) REVERT: H 141 ASP cc_start: 0.6190 (t70) cc_final: 0.5987 (t70) REVERT: H 142 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7543 (mttp) REVERT: H 210 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8966 (pt) REVERT: H 269 LEU cc_start: 0.8695 (mt) cc_final: 0.7992 (mt) REVERT: H 370 ASP cc_start: 0.7345 (t0) cc_final: 0.6919 (t70) REVERT: A 1 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7038 (mpp) REVERT: A 11 MET cc_start: 0.8055 (tpt) cc_final: 0.7683 (tpt) REVERT: A 48 PHE cc_start: 0.8835 (m-80) cc_final: 0.8597 (m-80) REVERT: A 91 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6169 (tm-30) REVERT: B 4 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6350 (ptm-80) REVERT: B 18 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7152 (mp10) REVERT: B 70 MET cc_start: 0.7081 (mmt) cc_final: 0.6869 (mmm) REVERT: B 80 ASP cc_start: 0.7319 (t0) cc_final: 0.6941 (t0) REVERT: B 89 GLN cc_start: 0.7042 (mt0) cc_final: 0.6317 (mt0) REVERT: B 113 LYS cc_start: 0.6289 (OUTLIER) cc_final: 0.5887 (mttm) REVERT: G 216 MET cc_start: 0.7753 (mpp) cc_final: 0.7469 (mpp) REVERT: G 261 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8862 (tt) REVERT: G 277 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7996 (mmm) REVERT: G 286 THR cc_start: 0.7524 (t) cc_final: 0.6945 (p) REVERT: G 306 GLU cc_start: 0.7142 (mp0) cc_final: 0.6733 (mm-30) REVERT: G 348 GLU cc_start: 0.7291 (mp0) cc_final: 0.6912 (mp0) REVERT: E 91 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6597 (tm-30) REVERT: F 91 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6907 (tm-30) REVERT: F 93 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8580 (mp) REVERT: I 44 ASP cc_start: 0.7554 (t0) cc_final: 0.7329 (t0) REVERT: I 49 GLU cc_start: 0.6829 (tp30) cc_final: 0.6307 (tt0) REVERT: I 139 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8348 (tp) outliers start: 109 outliers final: 87 residues processed: 389 average time/residue: 0.2572 time to fit residues: 159.9862 Evaluate side-chains 392 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 295 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 238 THR Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 388 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 0.0170 chunk 143 optimal weight: 8.9990 overall best weight: 1.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN G 234 ASN ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 1.0379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18501 Z= 0.186 Angle : 0.522 7.847 25161 Z= 0.270 Chirality : 0.044 0.204 2919 Planarity : 0.003 0.048 3264 Dihedral : 4.269 57.530 2513 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.49 % Favored : 96.38 % Rotamer: Outliers : 4.99 % Allowed : 29.53 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2319 helix: 1.49 (0.26), residues: 345 sheet: -0.69 (0.19), residues: 798 loop : -1.34 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 70 HIS 0.006 0.001 HIS I 318 PHE 0.014 0.001 PHE I 231 TYR 0.015 0.001 TYR G 280 ARG 0.004 0.000 ARG E 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4638 Ramachandran restraints generated. 2319 Oldfield, 0 Emsley, 2319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 299 time to evaluate : 1.982 Fit side-chains REVERT: C 62 TYR cc_start: 0.8744 (m-80) cc_final: 0.8425 (m-80) REVERT: D 14 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8239 (ttt180) REVERT: D 25 ASP cc_start: 0.8522 (m-30) cc_final: 0.8288 (m-30) REVERT: D 70 MET cc_start: 0.8208 (mmt) cc_final: 0.7875 (mmm) REVERT: D 91 GLU cc_start: 0.7948 (tp30) cc_final: 0.7553 (tm-30) REVERT: D 113 LYS cc_start: 0.6380 (mmtt) cc_final: 0.6129 (mttm) REVERT: H 136 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8553 (mt) REVERT: H 141 ASP cc_start: 0.6196 (t70) cc_final: 0.5977 (t70) REVERT: H 142 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7540 (mttp) REVERT: H 210 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (pt) REVERT: H 370 ASP cc_start: 0.7590 (t0) cc_final: 0.7337 (t70) REVERT: A 1 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: A 11 MET cc_start: 0.8028 (tpt) cc_final: 0.7680 (tpt) REVERT: A 48 PHE cc_start: 0.8815 (m-80) cc_final: 0.8571 (m-80) REVERT: A 91 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6148 (tm-30) REVERT: B 18 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: B 69 TRP cc_start: 0.9069 (m100) cc_final: 0.8106 (m100) REVERT: B 80 ASP cc_start: 0.7316 (t0) cc_final: 0.6947 (t0) REVERT: B 89 GLN cc_start: 0.7087 (mt0) cc_final: 0.6339 (mt0) REVERT: B 113 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5832 (mttm) REVERT: G 216 MET cc_start: 0.7614 (mpp) cc_final: 0.7372 (mpp) REVERT: G 261 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8930 (tt) REVERT: G 277 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7992 (mmm) REVERT: G 286 THR cc_start: 0.7401 (t) cc_final: 0.6831 (p) REVERT: G 306 GLU cc_start: 0.7163 (mp0) cc_final: 0.6729 (mm-30) REVERT: G 348 GLU cc_start: 0.7288 (mp0) cc_final: 0.6908 (mp0) REVERT: E 91 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6528 (tm-30) REVERT: F 91 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6889 (tm-30) REVERT: I 44 ASP cc_start: 0.7491 (t0) cc_final: 0.7254 (t0) REVERT: I 49 GLU cc_start: 0.6977 (tp30) cc_final: 0.6422 (tt0) REVERT: I 139 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8357 (tp) outliers start: 101 outliers final: 84 residues processed: 374 average time/residue: 0.2544 time to fit residues: 152.0203 Evaluate side-chains 388 residues out of total 2025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 296 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 133 MET Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 295 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 455 THR Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 99 SER Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 248 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 277 MET Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 342 ASP Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 192 ASP Chi-restraints excluded: chain I residue 241 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 380 THR Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain I residue 388 THR Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 430 LEU Chi-restraints excluded: chain I residue 455 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN ** G 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 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 = 0.3508 r_free = 0.3508 target = 0.134574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111962 restraints weight = 27883.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110984 restraints weight = 31595.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111919 restraints weight = 31723.374| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 1.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18501 Z= 0.205 Angle : 0.531 7.141 25161 Z= 0.275 Chirality : 0.044 0.152 2919 Planarity : 0.003 0.047 3264 Dihedral : 4.279 59.951 2513 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.88 % Favored : 95.99 % Rotamer: Outliers : 4.89 % Allowed : 29.83 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.99 (0.17), residues: 2319 helix: 1.54 (0.27), residues: 345 sheet: -0.56 (0.19), residues: 771 loop : -1.37 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 36 HIS 0.006 0.001 HIS I 318 PHE 0.012 0.001 PHE I 231 TYR 0.032 0.001 TYR G 303 ARG 0.004 0.000 ARG E 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3861.93 seconds wall clock time: 70 minutes 47.48 seconds (4247.48 seconds total)