Starting phenix.real_space_refine on Fri Feb 16 20:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqf_4981/02_2024/6rqf_4981_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqf_4981/02_2024/6rqf_4981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqf_4981/02_2024/6rqf_4981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqf_4981/02_2024/6rqf_4981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqf_4981/02_2024/6rqf_4981_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rqf_4981/02_2024/6rqf_4981_updated.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 77 5.16 5 C 10932 2.51 5 N 2493 2.21 5 O 2836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 20": "OD1" <-> "OD2" Residue "I TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "J PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K ASP 32": "OD1" <-> "OD2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 134": "OD1" <-> "OD2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 201": "NH1" <-> "NH2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K GLU 217": "OE1" <-> "OE2" Residue "K ASP 240": "OD1" <-> "OD2" Residue "K ASP 247": "OD1" <-> "OD2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 137": "NH1" <-> "NH2" Residue "L ASP 153": "OD1" <-> "OD2" Residue "L PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "M PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "O PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "O ASP 36": "OD1" <-> "OD2" Residue "P ARG 26": "NH1" <-> "NH2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 8": "OD1" <-> "OD2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ASP 196": "OD1" <-> "OD2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "E PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "G PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 33": "OD1" <-> "OD2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16359 Number of models: 1 Model: "" Number of chains: 28 Chain: "I" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1705 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "J" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 142} Chain: "K" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} Chain: "L" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1333 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "O" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1705 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "B" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1234 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 142} Chain: "C" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} Chain: "D" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1333 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 294 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 341 Unusual residues: {'6PL': 1, 'BCR': 1, 'CLA': 1, 'HEC': 1, 'HEM': 2, 'PL9': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'LMG': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 94 Unusual residues: {'HEC': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 403 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PGV': 1, 'PL9': 2, 'SQD': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'HEC': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5926 SG CYS L 107 108.778 54.950 47.392 1.00 75.56 S ATOM 6062 SG CYS L 125 108.320 58.649 46.624 1.00 66.59 S ATOM 13431 SG CYS D 107 49.863 66.471 69.878 1.00 75.56 S ATOM 13567 SG CYS D 125 49.529 63.014 68.324 1.00 66.59 S Time building chain proxies: 8.95, per 1000 atoms: 0.55 Number of scatterers: 16359 At special positions: 0 Unit cell: (142.71, 115.02, 135.255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 77 16.00 P 7 15.00 Mg 2 11.99 O 2836 8.00 N 2493 7.00 C 10932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.08 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.24 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE2 FES D 201 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 201 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 125 " pdb=" FES L 201 " pdb="FE2 FES L 201 " - pdb=" ND1 HIS L 128 " pdb="FE1 FES L 201 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 201 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 201 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 12 sheets defined 44.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'I' and resid 4 through 12 removed outlier: 3.859A pdb=" N GLU I 10 " --> pdb=" O ASP I 6 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 21 Processing helix chain 'I' and resid 33 through 56 removed outlier: 4.383A pdb=" N GLY I 37 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY I 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE I 52 " --> pdb=" O ALA I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 Processing helix chain 'I' and resid 79 through 107 removed outlier: 3.721A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 135 Processing helix chain 'I' and resid 142 through 157 Proline residue: I 155 - end of helix Processing helix chain 'I' and resid 161 through 170 Processing helix chain 'I' and resid 177 through 188 Processing helix chain 'I' and resid 190 through 209 Processing helix chain 'J' and resid 12 through 19 Processing helix chain 'J' and resid 39 through 56 Processing helix chain 'J' and resid 79 through 88 Proline residue: J 83 - end of helix Processing helix chain 'J' and resid 94 through 102 Processing helix chain 'J' and resid 105 through 114 removed outlier: 4.338A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL J 111 " --> pdb=" O GLY J 107 " (cutoff:3.500A) Proline residue: J 112 - end of helix Processing helix chain 'J' and resid 123 through 125 No H-bonds generated for 'chain 'J' and resid 123 through 125' Processing helix chain 'J' and resid 127 through 146 Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'K' and resid 20 through 23 Processing helix chain 'K' and resid 91 through 97 removed outlier: 4.125A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 282 removed outlier: 4.265A pdb=" N PHE K 256 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE K 257 " --> pdb=" O GLY K 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 39 Proline residue: L 29 - end of helix Proline residue: L 36 - end of helix Processing helix chain 'L' and resid 65 through 70 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 27 Processing helix chain 'N' and resid 2 through 32 Processing helix chain 'O' and resid 4 through 29 Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 3 through 25 Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 15 through 22 Processing helix chain 'A' and resid 32 through 56 removed outlier: 4.289A pdb=" N GLY A 37 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 106 removed outlier: 3.850A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 136 Processing helix chain 'A' and resid 142 through 157 Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 160 through 170 Proline residue: A 164 - end of helix removed outlier: 3.516A pdb=" N LEU A 169 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.955A pdb=" N THR A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 39 through 57 Processing helix chain 'B' and resid 79 through 88 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 94 through 114 removed outlier: 4.242A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.934A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 127 through 146 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 248 through 282 removed outlier: 4.088A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 39 removed outlier: 3.739A pdb=" N LEU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.606A pdb=" N SER E 6 " --> pdb=" O PHE E 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 34 Processing helix chain 'G' and resid 4 through 29 removed outlier: 3.671A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 3 through 25 Processing sheet with id= A, first strand: chain 'K' and resid 32 through 34 Processing sheet with id= B, first strand: chain 'K' and resid 38 through 40 removed outlier: 8.432A pdb=" N VAL K 39 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL K 244 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 73 through 76 removed outlier: 3.502A pdb=" N ALA K 73 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 203 through 207 Processing sheet with id= E, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.760A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 101 through 103 Processing sheet with id= G, first strand: chain 'C' and resid 32 through 34 Processing sheet with id= H, first strand: chain 'C' and resid 38 through 40 removed outlier: 7.939A pdb=" N VAL C 39 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL C 244 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 73 through 75 Processing sheet with id= J, first strand: chain 'C' and resid 182 through 184 Processing sheet with id= K, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= L, first strand: chain 'D' and resid 101 through 103 661 hydrogen bonds defined for protein. 1806 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: 4.23 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 6521 1.41 - 1.61: 10104 1.61 - 1.82: 123 1.82 - 2.03: 24 2.03 - 2.23: 24 Bond restraints: 16796 Sorted by residual: bond pdb=" C2D HEC A 303 " pdb=" C3D HEC A 303 " ideal model delta sigma weight residual 1.544 1.319 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C31 6PL E 101 " pdb=" O31 6PL E 101 " ideal model delta sigma weight residual 1.206 1.431 -0.225 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C31 6PL I 307 " pdb=" O31 6PL I 307 " ideal model delta sigma weight residual 1.206 1.430 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C11 6PL I 307 " pdb=" O11 6PL I 307 " ideal model delta sigma weight residual 1.207 1.431 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C31 6PL N 101 " pdb=" O31 6PL N 101 " ideal model delta sigma weight residual 1.206 1.429 -0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 16791 not shown) Histogram of bond angle deviations from ideal: 85.38 - 103.97: 414 103.97 - 122.56: 20312 122.56 - 141.15: 2133 141.15 - 159.74: 2 159.74 - 178.33: 20 Bond angle restraints: 22881 Sorted by residual: angle pdb=" S1 FES D 201 " pdb="FE2 FES D 201 " pdb=" S2 FES D 201 " ideal model delta sigma weight residual 104.33 89.82 14.51 1.14e+00 7.69e-01 1.62e+02 angle pdb=" S1 FES L 201 " pdb="FE2 FES L 201 " pdb=" S2 FES L 201 " ideal model delta sigma weight residual 104.33 89.83 14.50 1.14e+00 7.69e-01 1.62e+02 angle pdb=" S1 FES D 201 " pdb="FE1 FES D 201 " pdb=" S2 FES D 201 " ideal model delta sigma weight residual 104.33 89.80 14.53 1.20e+00 6.94e-01 1.47e+02 angle pdb=" S1 FES L 201 " pdb="FE1 FES L 201 " pdb=" S2 FES L 201 " ideal model delta sigma weight residual 104.33 89.82 14.51 1.20e+00 6.94e-01 1.46e+02 angle pdb="FE1 FES D 201 " pdb=" S2 FES D 201 " pdb="FE2 FES D 201 " ideal model delta sigma weight residual 75.66 89.09 -13.43 1.14e+00 7.69e-01 1.39e+02 ... (remaining 22876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 9150 27.08 - 54.15: 583 54.15 - 81.23: 102 81.23 - 108.31: 15 108.31 - 135.38: 8 Dihedral angle restraints: 9858 sinusoidal: 4324 harmonic: 5534 Sorted by residual: dihedral pdb=" C2C HEC K 301 " pdb=" C3C HEC K 301 " pdb=" CAC HEC K 301 " pdb=" CBC HEC K 301 " ideal model delta sinusoidal sigma weight residual 60.00 -22.26 82.26 2 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " pdb=" CAB HEC A 303 " pdb=" CBB HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 0.32 59.68 2 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual -120.00 -177.71 57.71 2 1.00e+01 1.00e-02 3.43e+01 ... (remaining 9855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2351 0.123 - 0.247: 116 0.247 - 0.370: 19 0.370 - 0.493: 0 0.493 - 0.616: 1 Chirality restraints: 2487 Sorted by residual: chirality pdb=" CA GLN A 177 " pdb=" N GLN A 177 " pdb=" C GLN A 177 " pdb=" CB GLN A 177 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.50e+00 chirality pdb=" C1 LMG F 101 " pdb=" C2 LMG F 101 " pdb=" O1 LMG F 101 " pdb=" O6 LMG F 101 " both_signs ideal model delta sigma weight residual False 2.29 2.64 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA SER A 174 " pdb=" N SER A 174 " pdb=" C SER A 174 " pdb=" CB SER A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2484 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PL9 A 306 " 0.086 2.00e-02 2.50e+03 2.03e-01 1.13e+03 pdb=" C2 PL9 A 306 " -0.005 2.00e-02 2.50e+03 pdb=" C3 PL9 A 306 " -0.076 2.00e-02 2.50e+03 pdb=" C4 PL9 A 306 " 0.107 2.00e-02 2.50e+03 pdb=" C5 PL9 A 306 " -0.012 2.00e-02 2.50e+03 pdb=" C52 PL9 A 306 " -0.071 2.00e-02 2.50e+03 pdb=" C53 PL9 A 306 " -0.273 2.00e-02 2.50e+03 pdb=" C6 PL9 A 306 " -0.064 2.00e-02 2.50e+03 pdb=" C7 PL9 A 306 " -0.351 2.00e-02 2.50e+03 pdb=" O1 PL9 A 306 " 0.371 2.00e-02 2.50e+03 pdb=" O2 PL9 A 306 " 0.287 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PL9 A 305 " -0.086 2.00e-02 2.50e+03 1.85e-01 9.42e+02 pdb=" C2 PL9 A 305 " -0.013 2.00e-02 2.50e+03 pdb=" C3 PL9 A 305 " 0.067 2.00e-02 2.50e+03 pdb=" C4 PL9 A 305 " -0.085 2.00e-02 2.50e+03 pdb=" C5 PL9 A 305 " -0.002 2.00e-02 2.50e+03 pdb=" C52 PL9 A 305 " 0.000 2.00e-02 2.50e+03 pdb=" C53 PL9 A 305 " 0.303 2.00e-02 2.50e+03 pdb=" C6 PL9 A 305 " 0.069 2.00e-02 2.50e+03 pdb=" C7 PL9 A 305 " 0.315 2.00e-02 2.50e+03 pdb=" O1 PL9 A 305 " -0.290 2.00e-02 2.50e+03 pdb=" O2 PL9 A 305 " -0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR I 305 " -0.046 2.00e-02 2.50e+03 2.56e-01 6.53e+02 pdb=" C11 BCR I 305 " 0.274 2.00e-02 2.50e+03 pdb=" C12 BCR I 305 " -0.395 2.00e-02 2.50e+03 pdb=" C13 BCR I 305 " 0.168 2.00e-02 2.50e+03 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 162 2.62 - 3.19: 13181 3.19 - 3.76: 24729 3.76 - 4.33: 33326 4.33 - 4.90: 56086 Nonbonded interactions: 127484 Sorted by model distance: nonbonded pdb=" O2 SQD A 307 " pdb=" O48 SQD A 307 " model vdw 2.053 2.440 nonbonded pdb=" C25 PL9 A 305 " pdb=" C20 PL9 A 306 " model vdw 2.210 3.880 nonbonded pdb=" O LEU C 69 " pdb=" OD1 ASN C 70 " model vdw 2.239 3.040 nonbonded pdb=" N GLY A 176 " pdb=" O GLY A 176 " model vdw 2.251 2.496 nonbonded pdb=" OH TYR I 58 " pdb=" O LEU I 138 " model vdw 2.265 2.440 ... (remaining 127479 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 215 or resid 301 through 304 or resid 306)) selection = (chain 'I' and (resid 1 through 215 or resid 301 through 304 or resid 306)) } ncs_group { reference = (chain 'B' and resid 1 through 160) selection = (chain 'J' and resid 1 through 160) } ncs_group { reference = (chain 'C' and (resid 1 through 285 or resid 301)) selection = (chain 'K' and (resid 1 through 285 or resid 301)) } ncs_group { reference = chain 'D' selection = (chain 'L' and (resid 1 through 179 or resid 201)) } ncs_group { reference = (chain 'E' and resid 1 through 31) selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = (chain 'N' and resid 1 through 36) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 1 through 29) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.470 Check model and map are aligned: 0.250 Set scattering table: 0.130 Process input model: 44.810 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.013 0.225 16796 Z= 0.758 Angle : 1.441 22.120 22881 Z= 0.700 Chirality : 0.064 0.616 2487 Planarity : 0.017 0.256 2778 Dihedral : 18.166 135.382 6308 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.24 % Favored : 95.40 % Rotamer: Outliers : 0.18 % Allowed : 9.49 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.15), residues: 1912 helix: -1.74 (0.13), residues: 905 sheet: -1.43 (0.31), residues: 215 loop : -2.58 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 68 HIS 0.007 0.002 HIS I 86 PHE 0.035 0.002 PHE I 131 TYR 0.014 0.002 TYR B 27 ARG 0.004 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 289 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: I 13 GLU cc_start: 0.8040 (mp0) cc_final: 0.7778 (mp0) REVERT: J 1 MET cc_start: 0.4961 (tpp) cc_final: 0.4244 (tmm) REVERT: L 117 ASN cc_start: 0.8892 (t0) cc_final: 0.8033 (t0) REVERT: M 12 LEU cc_start: 0.9303 (tt) cc_final: 0.8934 (mm) REVERT: P 26 ARG cc_start: 0.8948 (mtp180) cc_final: 0.8727 (mtp85) REVERT: A 1 MET cc_start: 0.5504 (mtt) cc_final: 0.4692 (mtm) REVERT: A 93 MET cc_start: 0.9123 (ttt) cc_final: 0.8801 (ttt) REVERT: A 96 MET cc_start: 0.9031 (mmt) cc_final: 0.8726 (mmt) REVERT: B 116 ASN cc_start: 0.8274 (m-40) cc_final: 0.7921 (m-40) REVERT: D 11 ASP cc_start: 0.7638 (p0) cc_final: 0.7357 (p0) REVERT: D 93 GLU cc_start: 0.8347 (mp0) cc_final: 0.8016 (mp0) REVERT: F 13 MET cc_start: 0.8846 (tpp) cc_final: 0.8441 (mmt) outliers start: 3 outliers final: 1 residues processed: 291 average time/residue: 0.3168 time to fit residues: 132.9269 Evaluate side-chains 223 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 GLN J 34 ASN K 25 HIS K 153 ASN K 168 ASN L 81 GLN L 104 ASN L 117 ASN A 15 GLN B 51 ASN B 86 GLN C 6 GLN C 23 ASN ** D 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16796 Z= 0.289 Angle : 0.724 19.646 22881 Z= 0.309 Chirality : 0.043 0.151 2487 Planarity : 0.006 0.076 2778 Dihedral : 16.483 124.370 2851 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.71 % Favored : 96.08 % Rotamer: Outliers : 1.97 % Allowed : 15.97 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.32 (0.18), residues: 1912 helix: 0.36 (0.17), residues: 900 sheet: -1.19 (0.33), residues: 212 loop : -2.24 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 146 HIS 0.013 0.002 HIS L 128 PHE 0.016 0.001 PHE I 131 TYR 0.012 0.001 TYR O 26 ARG 0.005 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 96 MET cc_start: 0.8806 (mmp) cc_final: 0.8568 (mmt) REVERT: A 1 MET cc_start: 0.5576 (mtt) cc_final: 0.4720 (mtm) REVERT: A 96 MET cc_start: 0.9099 (mmt) cc_final: 0.8813 (mmm) REVERT: D 117 ASN cc_start: 0.8774 (t0) cc_final: 0.8475 (t0) REVERT: D 168 ASP cc_start: 0.8915 (t0) cc_final: 0.8695 (t0) outliers start: 32 outliers final: 24 residues processed: 256 average time/residue: 0.2923 time to fit residues: 110.4412 Evaluate side-chains 248 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 104 ASN Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 0.0770 chunk 135 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN A 177 GLN C 23 ASN E 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16796 Z= 0.157 Angle : 0.617 19.042 22881 Z= 0.263 Chirality : 0.041 0.146 2487 Planarity : 0.005 0.065 2778 Dihedral : 15.245 122.991 2851 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.24 % Favored : 96.55 % Rotamer: Outliers : 2.10 % Allowed : 17.76 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.51 (0.19), residues: 1912 helix: 1.15 (0.18), residues: 898 sheet: -0.84 (0.33), residues: 212 loop : -1.98 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.012 0.001 PHE I 131 TYR 0.008 0.001 TYR D 132 ARG 0.006 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 199 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8422 (ttp) REVERT: J 15 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7610 (ttm110) REVERT: J 36 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8997 (tt) REVERT: A 1 MET cc_start: 0.5532 (mtt) cc_final: 0.4682 (mtm) REVERT: A 9 GLU cc_start: 0.9006 (tp30) cc_final: 0.8756 (tp30) REVERT: A 92 MET cc_start: 0.9051 (mmt) cc_final: 0.8666 (mmt) REVERT: A 96 MET cc_start: 0.9107 (mmt) cc_final: 0.8790 (mmm) REVERT: A 115 GLU cc_start: 0.8228 (mp0) cc_final: 0.8002 (mp0) REVERT: D 140 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8147 (ttt-90) REVERT: D 168 ASP cc_start: 0.9042 (t0) cc_final: 0.8828 (t0) REVERT: G 10 VAL cc_start: 0.9580 (t) cc_final: 0.9378 (p) outliers start: 34 outliers final: 22 residues processed: 261 average time/residue: 0.2810 time to fit residues: 110.6477 Evaluate side-chains 255 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 0.0060 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN L 117 ASN C 23 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN E 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16796 Z= 0.215 Angle : 0.625 18.913 22881 Z= 0.266 Chirality : 0.042 0.138 2487 Planarity : 0.004 0.058 2778 Dihedral : 14.818 128.072 2851 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.50 % Favored : 96.29 % Rotamer: Outliers : 3.08 % Allowed : 18.56 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1912 helix: 1.41 (0.18), residues: 900 sheet: -0.72 (0.34), residues: 212 loop : -1.81 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.007 0.001 HIS I 202 PHE 0.011 0.001 PHE I 131 TYR 0.011 0.001 TYR D 132 ARG 0.006 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 1.754 Fit side-chains revert: symmetry clash REVERT: I 199 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8459 (ttp) REVERT: J 15 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7578 (ttm110) REVERT: J 36 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9024 (tt) REVERT: A 1 MET cc_start: 0.5531 (mtt) cc_final: 0.4678 (mtm) REVERT: A 9 GLU cc_start: 0.8985 (tp30) cc_final: 0.8781 (tp30) REVERT: A 92 MET cc_start: 0.9106 (mmt) cc_final: 0.8679 (mmt) REVERT: A 96 MET cc_start: 0.9118 (mmt) cc_final: 0.8788 (mmm) REVERT: A 159 PRO cc_start: 0.7897 (Cg_exo) cc_final: 0.7674 (Cg_endo) REVERT: B 22 MET cc_start: 0.8957 (mtm) cc_final: 0.8718 (mtp) REVERT: E 21 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8061 (mp) outliers start: 50 outliers final: 35 residues processed: 259 average time/residue: 0.2628 time to fit residues: 103.6308 Evaluate side-chains 263 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 14 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 16796 Z= 0.467 Angle : 0.777 23.330 22881 Z= 0.329 Chirality : 0.046 0.142 2487 Planarity : 0.005 0.060 2778 Dihedral : 15.234 136.373 2851 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 3.88 % Allowed : 19.48 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.34 (0.19), residues: 1912 helix: 1.28 (0.18), residues: 892 sheet: -0.88 (0.34), residues: 218 loop : -1.82 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 146 HIS 0.011 0.002 HIS I 202 PHE 0.017 0.002 PHE I 131 TYR 0.014 0.002 TYR D 132 ARG 0.006 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 217 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: I 199 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8696 (ttp) REVERT: J 15 ARG cc_start: 0.7854 (ttt180) cc_final: 0.7617 (ttm110) REVERT: J 36 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9076 (tt) REVERT: K 171 TYR cc_start: 0.6659 (m-80) cc_final: 0.6102 (m-80) REVERT: O 31 ARG cc_start: 0.8210 (mmt90) cc_final: 0.7481 (ptm160) REVERT: A 1 MET cc_start: 0.5438 (mtt) cc_final: 0.4602 (mtm) REVERT: A 92 MET cc_start: 0.9228 (mmt) cc_final: 0.8887 (mmt) REVERT: A 96 MET cc_start: 0.9114 (mmt) cc_final: 0.8828 (mmm) REVERT: B 22 MET cc_start: 0.9095 (mtm) cc_final: 0.8835 (mtp) REVERT: E 21 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8181 (mp) REVERT: F 5 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 2 ILE cc_start: 0.8799 (mt) cc_final: 0.8579 (tt) outliers start: 63 outliers final: 51 residues processed: 259 average time/residue: 0.2612 time to fit residues: 103.1466 Evaluate side-chains 264 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 210 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN C 23 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16796 Z= 0.210 Angle : 0.635 20.778 22881 Z= 0.267 Chirality : 0.042 0.137 2487 Planarity : 0.004 0.056 2778 Dihedral : 14.516 138.203 2851 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 3.08 % Allowed : 20.35 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.01 (0.19), residues: 1912 helix: 1.61 (0.18), residues: 890 sheet: -0.70 (0.34), residues: 220 loop : -1.69 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 PHE 0.012 0.001 PHE A 183 TYR 0.011 0.001 TYR K 190 ARG 0.006 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 199 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8587 (ttp) REVERT: I 205 MET cc_start: 0.8526 (mtt) cc_final: 0.8140 (mtt) REVERT: J 36 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9061 (tt) REVERT: O 31 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7475 (ptm160) REVERT: A 1 MET cc_start: 0.5373 (mtt) cc_final: 0.4576 (mtm) REVERT: A 92 MET cc_start: 0.9131 (mmt) cc_final: 0.8868 (mmt) REVERT: A 96 MET cc_start: 0.9107 (mmt) cc_final: 0.8805 (mmm) REVERT: A 115 GLU cc_start: 0.8157 (mp0) cc_final: 0.7609 (mt-10) REVERT: B 22 MET cc_start: 0.8971 (mtm) cc_final: 0.8715 (mtp) REVERT: E 21 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8133 (mp) outliers start: 50 outliers final: 40 residues processed: 261 average time/residue: 0.2638 time to fit residues: 104.6084 Evaluate side-chains 263 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16796 Z= 0.193 Angle : 0.625 19.407 22881 Z= 0.267 Chirality : 0.042 0.239 2487 Planarity : 0.004 0.058 2778 Dihedral : 14.107 140.182 2851 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.03 % Favored : 95.76 % Rotamer: Outliers : 3.27 % Allowed : 20.96 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1912 helix: 1.81 (0.18), residues: 879 sheet: -0.74 (0.32), residues: 244 loop : -1.50 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 PHE 0.010 0.001 PHE I 131 TYR 0.013 0.001 TYR G 26 ARG 0.008 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 225 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 199 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8550 (ttp) REVERT: I 205 MET cc_start: 0.8464 (mtt) cc_final: 0.8136 (mtt) REVERT: J 1 MET cc_start: 0.4986 (tmm) cc_final: 0.4258 (tmm) REVERT: J 36 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9026 (tt) REVERT: J 58 GLU cc_start: 0.8172 (tp30) cc_final: 0.7787 (tp30) REVERT: L 14 LYS cc_start: 0.7767 (mttm) cc_final: 0.7324 (mttm) REVERT: L 132 TYR cc_start: 0.8823 (m-80) cc_final: 0.8507 (m-80) REVERT: O 31 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7477 (ptm160) REVERT: A 1 MET cc_start: 0.5360 (mtt) cc_final: 0.4538 (mtm) REVERT: A 92 MET cc_start: 0.9099 (mmt) cc_final: 0.8804 (mmt) REVERT: A 96 MET cc_start: 0.9110 (mmt) cc_final: 0.8785 (mmm) REVERT: A 97 MET cc_start: 0.8227 (ttp) cc_final: 0.7979 (ttp) REVERT: A 115 GLU cc_start: 0.8141 (mp0) cc_final: 0.7629 (mt-10) REVERT: C 160 TYR cc_start: 0.9249 (m-80) cc_final: 0.8961 (m-80) REVERT: D 140 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8043 (ttt-90) REVERT: E 21 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8089 (mp) outliers start: 53 outliers final: 42 residues processed: 263 average time/residue: 0.2645 time to fit residues: 106.4377 Evaluate side-chains 264 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 219 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 54 optimal weight: 0.0670 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 88 optimal weight: 0.0370 chunk 16 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16796 Z= 0.146 Angle : 0.590 17.239 22881 Z= 0.256 Chirality : 0.041 0.141 2487 Planarity : 0.004 0.058 2778 Dihedral : 13.599 142.480 2851 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % Rotamer: Outliers : 2.34 % Allowed : 22.13 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1912 helix: 1.96 (0.18), residues: 886 sheet: -0.60 (0.32), residues: 243 loop : -1.46 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 7 HIS 0.004 0.001 HIS I 86 PHE 0.010 0.001 PHE A 183 TYR 0.012 0.001 TYR K 190 ARG 0.008 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 20 ASP cc_start: 0.8813 (t0) cc_final: 0.8591 (t0) REVERT: I 106 LEU cc_start: 0.9234 (mt) cc_final: 0.9007 (mt) REVERT: I 199 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8419 (ttp) REVERT: I 205 MET cc_start: 0.8406 (mtt) cc_final: 0.8088 (mtt) REVERT: J 1 MET cc_start: 0.5438 (tmm) cc_final: 0.5001 (tmm) REVERT: J 36 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9004 (tt) REVERT: L 14 LYS cc_start: 0.7565 (mttm) cc_final: 0.7170 (mttm) REVERT: L 132 TYR cc_start: 0.8796 (m-80) cc_final: 0.8486 (m-80) REVERT: O 31 ARG cc_start: 0.8234 (mmt90) cc_final: 0.7494 (ptm160) REVERT: A 1 MET cc_start: 0.5332 (mtt) cc_final: 0.4511 (mtm) REVERT: A 96 MET cc_start: 0.9111 (mmt) cc_final: 0.8774 (mmm) REVERT: A 115 GLU cc_start: 0.8116 (mp0) cc_final: 0.7511 (mt-10) REVERT: C 160 TYR cc_start: 0.9184 (m-80) cc_final: 0.8959 (m-80) REVERT: E 21 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8095 (mp) outliers start: 38 outliers final: 29 residues processed: 266 average time/residue: 0.2691 time to fit residues: 109.8880 Evaluate side-chains 255 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.5980 chunk 171 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 0.0030 chunk 166 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16796 Z= 0.167 Angle : 0.603 17.836 22881 Z= 0.261 Chirality : 0.042 0.289 2487 Planarity : 0.004 0.058 2778 Dihedral : 13.401 143.819 2851 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.66 % Favored : 96.13 % Rotamer: Outliers : 2.47 % Allowed : 22.32 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.50 (0.20), residues: 1912 helix: 2.00 (0.18), residues: 890 sheet: -0.58 (0.32), residues: 244 loop : -1.40 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.012 0.001 PHE J 124 TYR 0.012 0.001 TYR G 26 ARG 0.009 0.000 ARG D 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 106 LEU cc_start: 0.9212 (mt) cc_final: 0.9006 (mt) REVERT: I 199 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: I 205 MET cc_start: 0.8424 (mtt) cc_final: 0.8121 (mtt) REVERT: J 36 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9010 (tt) REVERT: J 58 GLU cc_start: 0.8198 (tp30) cc_final: 0.7858 (tp30) REVERT: L 14 LYS cc_start: 0.7666 (mttm) cc_final: 0.7217 (mttm) REVERT: L 132 TYR cc_start: 0.8796 (m-80) cc_final: 0.8485 (m-80) REVERT: O 31 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7533 (ptm160) REVERT: A 1 MET cc_start: 0.5342 (mtt) cc_final: 0.4519 (mtm) REVERT: A 96 MET cc_start: 0.9103 (mmt) cc_final: 0.8758 (mmm) REVERT: A 97 MET cc_start: 0.8178 (ttp) cc_final: 0.7946 (ttp) REVERT: A 115 GLU cc_start: 0.8126 (mp0) cc_final: 0.7500 (mt-10) REVERT: C 160 TYR cc_start: 0.9186 (m-80) cc_final: 0.8958 (m-80) REVERT: E 21 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8080 (mp) outliers start: 40 outliers final: 35 residues processed: 256 average time/residue: 0.2633 time to fit residues: 104.5189 Evaluate side-chains 261 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.0970 chunk 176 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN L 81 GLN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16796 Z= 0.152 Angle : 0.592 17.354 22881 Z= 0.257 Chirality : 0.041 0.241 2487 Planarity : 0.004 0.058 2778 Dihedral : 13.113 145.139 2851 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 2.28 % Allowed : 22.38 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.60 (0.20), residues: 1912 helix: 2.06 (0.18), residues: 892 sheet: -0.54 (0.33), residues: 236 loop : -1.31 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 7 HIS 0.004 0.001 HIS I 202 PHE 0.011 0.001 PHE J 124 TYR 0.012 0.001 TYR G 26 ARG 0.010 0.000 ARG D 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 199 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8407 (ttp) REVERT: I 205 MET cc_start: 0.8420 (mtt) cc_final: 0.8122 (mtt) REVERT: J 36 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9008 (tt) REVERT: J 58 GLU cc_start: 0.8202 (tp30) cc_final: 0.7886 (tp30) REVERT: L 14 LYS cc_start: 0.7575 (mttm) cc_final: 0.7143 (mttm) REVERT: L 132 TYR cc_start: 0.8782 (m-80) cc_final: 0.8464 (m-80) REVERT: O 31 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7472 (ptm160) REVERT: A 1 MET cc_start: 0.5329 (mtt) cc_final: 0.4510 (mtm) REVERT: A 96 MET cc_start: 0.9086 (mmt) cc_final: 0.8755 (mmm) REVERT: A 97 MET cc_start: 0.8212 (ttp) cc_final: 0.7798 (ttp) REVERT: A 115 GLU cc_start: 0.8070 (mp0) cc_final: 0.7484 (mt-10) REVERT: C 160 TYR cc_start: 0.9159 (m-80) cc_final: 0.8940 (m-80) outliers start: 37 outliers final: 35 residues processed: 264 average time/residue: 0.2669 time to fit residues: 109.1524 Evaluate side-chains 263 residues out of total 1622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 226 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 199 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 51 ASN Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 162 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 19 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain H residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 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 = 0.3304 r_free = 0.3304 target = 0.104995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.078425 restraints weight = 29866.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.081006 restraints weight = 15935.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.082659 restraints weight = 11220.043| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16796 Z= 0.217 Angle : 0.629 19.073 22881 Z= 0.270 Chirality : 0.042 0.256 2487 Planarity : 0.004 0.058 2778 Dihedral : 13.210 146.259 2851 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.71 % Favored : 96.13 % Rotamer: Outliers : 2.65 % Allowed : 21.95 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.59 (0.20), residues: 1912 helix: 2.04 (0.18), residues: 896 sheet: -0.56 (0.32), residues: 244 loop : -1.32 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 146 HIS 0.006 0.001 HIS I 202 PHE 0.013 0.001 PHE J 124 TYR 0.011 0.001 TYR G 26 ARG 0.010 0.000 ARG D 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.47 seconds wall clock time: 59 minutes 25.27 seconds (3565.27 seconds total)