Starting phenix.real_space_refine on Wed Feb 21 21:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wmt_21852/02_2024/6wmt_21852_neut_trim_updated.pdb" } resolution = 4.43 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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 Zn 2 6.06 5 P 123 5.49 5 Mg 2 5.21 5 S 118 5.16 5 C 19784 2.51 5 N 5554 2.21 5 O 6348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 401": "OD1" <-> "OD2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ASP 440": "OD1" <-> "OD2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 551": "NH1" <-> "NH2" Residue "C TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 583": "NH1" <-> "NH2" Residue "C TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 615": "OD1" <-> "OD2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "C ASP 657": "OD1" <-> "OD2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C GLU 729": "OE1" <-> "OE2" Residue "C PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 816": "OD1" <-> "OD2" Residue "C TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1200": "OD1" <-> "OD2" Residue "C PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1234": "OD1" <-> "OD2" Residue "C TYR 1243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1284": "OE1" <-> "OE2" Residue "C ARG 1313": "NH1" <-> "NH2" Residue "C GLU 1341": "OE1" <-> "OE2" Residue "C ARG 1343": "NH1" <-> "NH2" Residue "C TYR 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D ARG 429": "NH1" <-> "NH2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 513": "NH1" <-> "NH2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 656": "OE1" <-> "OE2" Residue "D GLU 673": "OE1" <-> "OE2" Residue "D ARG 728": "NH1" <-> "NH2" Residue "D TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 799": "OD1" <-> "OD2" Residue "D ARG 839": "NH1" <-> "NH2" Residue "D GLU 909": "OE1" <-> "OE2" Residue "D GLU 1242": "OE1" <-> "OE2" Residue "D ASP 1256": "OD1" <-> "OD2" Residue "D TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1299": "NH1" <-> "NH2" Residue "D PHE 1307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1315": "OE1" <-> "OE2" Residue "D ARG 1318": "NH1" <-> "NH2" Residue "D ARG 1343": "NH1" <-> "NH2" Residue "D ARG 1354": "NH1" <-> "NH2" Residue "M TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 9": "OD1" <-> "OD2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M ASP 59": "OD1" <-> "OD2" Residue "M PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 116": "OD1" <-> "OD2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 186": "OE1" <-> "OE2" Residue "S PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 102": "OD1" <-> "OD2" Residue "Z TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 161": "NH1" <-> "NH2" Residue "Z TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 225": "OE1" <-> "OE2" Residue "Z PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 271": "OE1" <-> "OE2" Residue "Z PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 333": "OE1" <-> "OE2" Residue "Z TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 409": "OD1" <-> "OD2" Residue "Z ARG 429": "NH1" <-> "NH2" Residue "Z ARG 440": "NH1" <-> "NH2" Residue "Z ASP 486": "OD1" <-> "OD2" Residue "Z GLU 521": "OE1" <-> "OE2" Residue "Z GLU 541": "OE1" <-> "OE2" Residue "Z PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31931 Number of models: 1 Model: "" Number of chains: 17 Chain: "E" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 68} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1769 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 8926 Classifications: {'peptide': 1187} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 42, 'TRANS': 1144} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 23, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 214 Chain: "D" Number of atoms: 8874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8874 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1117} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 115 Chain: "G" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1069 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "H" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 852 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "K" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'CIS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 365 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'CIS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'UNK:plan-1': 73} Unresolved non-hydrogen planarities: 73 Chain: "M" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1598 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 189} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "S" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1583 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "X" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "Z" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3772 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 456} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' MG': 1, ' ZN': 2, 'G4P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'G4P': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.55, per 1000 atoms: 0.52 Number of scatterers: 31931 At special positions: 0 Unit cell: (181.9, 187.25, 147.66, 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) Zn 2 29.99 S 118 16.00 P 123 15.00 Mg 2 11.99 O 6348 8.00 N 5554 7.00 C 19784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.44 Conformation dependent library (CDL) restraints added in 4.8 seconds 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 25 sheets defined 44.6% alpha, 8.1% beta 21 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 16.77 Creating SS restraints... Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.659A pdb=" N ASP E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 12' Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 47 through 57 Processing helix chain 'E' and resid 62 through 71 removed outlier: 3.541A pdb=" N LEU E 66 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 69 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.654A pdb=" N LEU A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 206 through 226 removed outlier: 4.170A pdb=" N VAL A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.727A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 27 through 39 removed outlier: 4.436A pdb=" N ILE C 30 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 33 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 34 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 removed outlier: 3.627A pdb=" N SER C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 348 through 355 Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.800A pdb=" N PHE C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 425 through 440 Processing helix chain 'C' and resid 459 through 483 removed outlier: 4.206A pdb=" N SER C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 511 removed outlier: 3.526A pdb=" N ALA C 503 " --> pdb=" O LYS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 531 Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 611 through 616 removed outlier: 4.165A pdb=" N ASN C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 662 No H-bonds generated for 'chain 'C' and resid 660 through 662' Processing helix chain 'C' and resid 666 through 670 removed outlier: 3.709A pdb=" N LEU C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 666 through 670' Processing helix chain 'C' and resid 679 through 691 removed outlier: 3.681A pdb=" N ARG C 690 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 823 through 827 Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 899 through 908 Processing helix chain 'C' and resid 945 through 979 Processing helix chain 'C' and resid 1024 through 1027 No H-bonds generated for 'chain 'C' and resid 1024 through 1027' Processing helix chain 'C' and resid 1031 through 1047 Processing helix chain 'C' and resid 1114 through 1119 Proline residue: C1118 - end of helix No H-bonds generated for 'chain 'C' and resid 1114 through 1119' Processing helix chain 'C' and resid 1123 through 1147 Processing helix chain 'C' and resid 1152 through 1164 Processing helix chain 'C' and resid 1173 through 1175 No H-bonds generated for 'chain 'C' and resid 1173 through 1175' Processing helix chain 'C' and resid 1178 through 1187 Processing helix chain 'C' and resid 1204 through 1214 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1296 through 1304 Processing helix chain 'C' and resid 1310 through 1322 Processing helix chain 'C' and resid 1333 through 1344 Processing helix chain 'D' and resid 25 through 31 Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 93 through 98 Processing helix chain 'D' and resid 112 through 115 No H-bonds generated for 'chain 'D' and resid 112 through 115' Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'D' and resid 192 through 204 Processing helix chain 'D' and resid 211 through 228 removed outlier: 4.117A pdb=" N ALA D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 262 through 283 Processing helix chain 'D' and resid 287 through 305 Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.626A pdb=" N ILE D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 329' Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 368 through 374 Processing helix chain 'D' and resid 376 through 386 Processing helix chain 'D' and resid 392 through 400 Processing helix chain 'D' and resid 404 through 413 removed outlier: 3.940A pdb=" N ASP D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 449 through 455 removed outlier: 4.119A pdb=" N ALA D 453 " --> pdb=" O PRO D 449 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 528 through 537 Processing helix chain 'D' and resid 572 through 578 Processing helix chain 'D' and resid 596 through 609 Processing helix chain 'D' and resid 612 through 633 Processing helix chain 'D' and resid 648 through 668 Processing helix chain 'D' and resid 673 through 700 removed outlier: 3.666A pdb=" N ASP D 697 " --> pdb=" O ALA D 693 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 698 " --> pdb=" O SER D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 725 Processing helix chain 'D' and resid 731 through 738 Processing helix chain 'D' and resid 766 through 801 removed outlier: 3.855A pdb=" N HIS D 774 " --> pdb=" O PHE D 770 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY D 775 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 787 " --> pdb=" O THR D 783 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN D 789 " --> pdb=" O LEU D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 832 through 836 Processing helix chain 'D' and resid 862 through 871 removed outlier: 4.127A pdb=" N LEU D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 895 No H-bonds generated for 'chain 'D' and resid 892 through 895' Processing helix chain 'D' and resid 911 through 925 Proline residue: D 922 - end of helix removed outlier: 4.597A pdb=" N GLN D 925 " --> pdb=" O GLU D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 1125 through 1133 Processing helix chain 'D' and resid 1205 through 1211 removed outlier: 3.759A pdb=" N LEU D1209 " --> pdb=" O PRO D1205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D1210 " --> pdb=" O HIS D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1213 through 1231 removed outlier: 3.505A pdb=" N PHE D1217 " --> pdb=" O GLY D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1238 through 1248 removed outlier: 3.728A pdb=" N ILE D1244 " --> pdb=" O HIS D1240 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D1247 " --> pdb=" O THR D1243 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1279 Processing helix chain 'D' and resid 1297 through 1302 Processing helix chain 'D' and resid 1307 through 1313 Processing helix chain 'D' and resid 1316 through 1326 removed outlier: 3.571A pdb=" N ILE D1325 " --> pdb=" O THR D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1335 through 1340 Processing helix chain 'D' and resid 1349 through 1364 removed outlier: 3.660A pdb=" N MET D1363 " --> pdb=" O LYS D1359 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D1364 " --> pdb=" O ILE D1360 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 254 No H-bonds generated for 'chain 'K' and resid 251 through 254' Processing helix chain 'K' and resid 257 through 260 Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'K' and resid 278 through 283 Processing helix chain 'K' and resid 286 through 291 Processing helix chain 'K' and resid 297 through 310 Processing helix chain 'L' and resid 251 through 254 No H-bonds generated for 'chain 'L' and resid 251 through 254' Processing helix chain 'L' and resid 257 through 260 Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'L' and resid 278 through 283 Processing helix chain 'L' and resid 286 through 291 Processing helix chain 'L' and resid 297 through 310 Processing helix chain 'M' and resid 10 through 22 Processing helix chain 'M' and resid 34 through 46 removed outlier: 3.608A pdb=" N SER M 37 " --> pdb=" O GLU M 34 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS M 38 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS M 39 " --> pdb=" O ASN M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 75 Processing helix chain 'M' and resid 86 through 111 removed outlier: 3.982A pdb=" N GLN M 105 " --> pdb=" O LYS M 101 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 148 removed outlier: 4.199A pdb=" N ILE M 132 " --> pdb=" O GLN M 128 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER M 133 " --> pdb=" O ARG M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 172 Processing helix chain 'M' and resid 181 through 191 Processing helix chain 'M' and resid 194 through 200 removed outlier: 3.692A pdb=" N LYS M 198 " --> pdb=" O PRO M 194 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR M 199 " --> pdb=" O ASN M 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 39 through 45 Processing helix chain 'S' and resid 64 through 74 removed outlier: 4.087A pdb=" N LEU S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ILE S 69 " --> pdb=" O LYS S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 100 Processing helix chain 'S' and resid 103 through 111 removed outlier: 3.708A pdb=" N GLN S 108 " --> pdb=" O PRO S 104 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE S 109 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 134 Processing helix chain 'S' and resid 150 through 165 removed outlier: 3.527A pdb=" N ALA S 157 " --> pdb=" O CYS S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 185 removed outlier: 3.758A pdb=" N LYS S 181 " --> pdb=" O TYR S 177 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG S 182 " --> pdb=" O GLU S 178 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE S 184 " --> pdb=" O LYS S 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA S 185 " --> pdb=" O LYS S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 209 Processing helix chain 'Z' and resid 87 through 97 removed outlier: 3.564A pdb=" N GLU Z 94 " --> pdb=" O MET Z 90 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE Z 97 " --> pdb=" O ARG Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 126 Processing helix chain 'Z' and resid 128 through 150 removed outlier: 3.609A pdb=" N LYS Z 132 " --> pdb=" O PRO Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 212 Processing helix chain 'Z' and resid 217 through 228 Processing helix chain 'Z' and resid 234 through 264 Proline residue: Z 246 - end of helix removed outlier: 3.831A pdb=" N GLU Z 263 " --> pdb=" O ARG Z 259 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG Z 264 " --> pdb=" O LEU Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 276 Processing helix chain 'Z' and resid 283 through 289 removed outlier: 3.933A pdb=" N LYS Z 289 " --> pdb=" O GLU Z 285 " (cutoff:3.500A) Processing helix chain 'Z' and resid 295 through 315 Processing helix chain 'Z' and resid 319 through 356 removed outlier: 4.085A pdb=" N VAL Z 325 " --> pdb=" O GLU Z 321 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA Z 346 " --> pdb=" O GLU Z 342 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN Z 347 " --> pdb=" O MET Z 343 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ARG Z 349 " --> pdb=" O GLU Z 345 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU Z 350 " --> pdb=" O ALA Z 346 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL Z 351 " --> pdb=" O ASN Z 347 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL Z 352 " --> pdb=" O LEU Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 382 removed outlier: 3.909A pdb=" N ASP Z 381 " --> pdb=" O MET Z 377 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS Z 382 " --> pdb=" O LYS Z 378 " (cutoff:3.500A) Processing helix chain 'Z' and resid 391 through 410 removed outlier: 3.599A pdb=" N TRP Z 398 " --> pdb=" O TYR Z 394 " (cutoff:3.500A) Processing helix chain 'Z' and resid 418 through 438 Processing helix chain 'Z' and resid 444 through 450 removed outlier: 3.678A pdb=" N HIS Z 450 " --> pdb=" O GLU Z 446 " (cutoff:3.500A) Processing helix chain 'Z' and resid 457 through 462 Processing helix chain 'Z' and resid 484 through 487 No H-bonds generated for 'chain 'Z' and resid 484 through 487' Processing helix chain 'Z' and resid 496 through 515 removed outlier: 3.710A pdb=" N LEU Z 502 " --> pdb=" O GLU Z 498 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS Z 510 " --> pdb=" O ARG Z 506 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU Z 511 " --> pdb=" O GLU Z 507 " (cutoff:3.500A) Processing helix chain 'Z' and resid 520 through 529 Processing helix chain 'Z' and resid 539 through 546 Processing helix chain 'Z' and resid 552 through 564 Processing helix chain 'Z' and resid 567 through 575 removed outlier: 4.460A pdb=" N PHE Z 572 " --> pdb=" O SER Z 568 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR Z 575 " --> pdb=" O ALA Z 571 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.066A pdb=" N LYS A 17 " --> pdb=" O LYS A 26 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 26 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.763A pdb=" N SER A 148 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 146 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 60 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 144 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE A 62 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER A 142 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 11 through 16 removed outlier: 4.419A pdb=" N ASN B 11 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 27 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 97 through 101 removed outlier: 3.712A pdb=" N SER B 56 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU B 146 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL B 54 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY B 148 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA B 52 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.235A pdb=" N VAL C 101 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR C 128 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU C 103 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR C 126 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= G, first strand: chain 'C' and resid 153 through 156 Processing sheet with id= H, first strand: chain 'C' and resid 160 through 164 removed outlier: 5.232A pdb=" N PHE C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 606 through 610 Processing sheet with id= J, first strand: chain 'C' and resid 636 through 640 Processing sheet with id= K, first strand: chain 'C' and resid 750 through 754 removed outlier: 3.515A pdb=" N ASP C 731 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS C 738 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL C 727 " --> pdb=" O LYS C 738 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 889 through 891 Processing sheet with id= M, first strand: chain 'C' and resid 1087 through 1089 removed outlier: 3.692A pdb=" N LEU C1245 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 818 through 820 removed outlier: 8.196A pdb=" N LEU C 820 " --> pdb=" O SER C1091 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL C1093 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 831 through 843 removed outlier: 3.820A pdb=" N ASN C 932 " --> pdb=" O PHE C1067 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA C1069 " --> pdb=" O VAL C 930 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 930 " --> pdb=" O ALA C1069 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 17 through 19 Processing sheet with id= Q, first strand: chain 'D' and resid 239 through 242 removed outlier: 7.575A pdb=" N HIS D 102 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU D 35 " --> pdb=" O HIS D 102 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP D 104 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 348 through 352 Processing sheet with id= S, first strand: chain 'D' and resid 545 through 549 Processing sheet with id= T, first strand: chain 'D' and resid 552 through 555 Processing sheet with id= U, first strand: chain 'D' and resid 701 through 704 Processing sheet with id= V, first strand: chain 'D' and resid 817 through 820 Processing sheet with id= W, first strand: chain 'D' and resid 1265 through 1267 removed outlier: 6.294A pdb=" N GLU D1289 " --> pdb=" O LEU D1255 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= Y, first strand: chain 'S' and resid 5 through 8 removed outlier: 6.291A pdb=" N ASP S 30 " --> pdb=" O LEU S 6 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR S 8 " --> pdb=" O ASP S 30 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL S 32 " --> pdb=" O THR S 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 1169 hydrogen bonds defined for protein. 3378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 13.22 Time building geometry restraints manager: 16.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6260 1.33 - 1.45: 7462 1.45 - 1.57: 18460 1.57 - 1.69: 239 1.69 - 1.81: 204 Bond restraints: 32625 Sorted by residual: bond pdb=" C2' G4P M 301 " pdb=" C1' G4P M 301 " ideal model delta sigma weight residual 1.305 1.520 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C2' G4P D1704 " pdb=" C1' G4P D1704 " ideal model delta sigma weight residual 1.305 1.518 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" O4' G4P M 301 " pdb=" C1' G4P M 301 " ideal model delta sigma weight residual 1.613 1.429 0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" O4' G4P D1704 " pdb=" C1' G4P D1704 " ideal model delta sigma weight residual 1.613 1.430 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" N3 G4P M 301 " pdb=" C4 G4P M 301 " ideal model delta sigma weight residual 1.494 1.353 0.141 2.00e-02 2.50e+03 4.97e+01 ... (remaining 32620 not shown) Histogram of bond angle deviations from ideal: 98.44 - 106.00: 1063 106.00 - 113.56: 18446 113.56 - 121.12: 16727 121.12 - 128.68: 8205 128.68 - 136.24: 178 Bond angle restraints: 44619 Sorted by residual: angle pdb=" O3' DA H 33 " pdb=" C3' DA H 33 " pdb=" C2' DA H 33 " ideal model delta sigma weight residual 111.50 102.07 9.43 1.50e+00 4.44e-01 3.96e+01 angle pdb=" N PRO M 77 " pdb=" CA PRO M 77 " pdb=" C PRO M 77 " ideal model delta sigma weight residual 114.92 107.52 7.40 1.19e+00 7.06e-01 3.87e+01 angle pdb=" O3' DC H 21 " pdb=" C3' DC H 21 " pdb=" C2' DC H 21 " ideal model delta sigma weight residual 111.50 102.19 9.31 1.50e+00 4.44e-01 3.85e+01 angle pdb=" O3' DT G 19 " pdb=" C3' DT G 19 " pdb=" C2' DT G 19 " ideal model delta sigma weight residual 111.50 102.19 9.31 1.50e+00 4.44e-01 3.85e+01 angle pdb=" O3' DG G 20 " pdb=" C3' DG G 20 " pdb=" C2' DG G 20 " ideal model delta sigma weight residual 111.50 102.27 9.23 1.50e+00 4.44e-01 3.79e+01 ... (remaining 44614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 19201 34.74 - 69.49: 483 69.49 - 104.23: 11 104.23 - 138.98: 5 138.98 - 173.72: 4 Dihedral angle restraints: 19704 sinusoidal: 8407 harmonic: 11297 Sorted by residual: dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PRO D 119 " pdb=" CA PRO D 119 " ideal model delta harmonic sigma weight residual 0.00 29.78 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" C LYS D 212 " pdb=" N LYS D 212 " pdb=" CA LYS D 212 " pdb=" CB LYS D 212 " ideal model delta harmonic sigma weight residual -122.60 -134.29 11.69 0 2.50e+00 1.60e-01 2.19e+01 dihedral pdb=" C GLN D 917 " pdb=" N GLN D 917 " pdb=" CA GLN D 917 " pdb=" CB GLN D 917 " ideal model delta harmonic sigma weight residual -122.60 -133.21 10.61 0 2.50e+00 1.60e-01 1.80e+01 ... (remaining 19701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2183 0.077 - 0.154: 2083 0.154 - 0.230: 887 0.230 - 0.307: 59 0.307 - 0.384: 5 Chirality restraints: 5217 Sorted by residual: chirality pdb=" CA LYS D 212 " pdb=" N LYS D 212 " pdb=" C LYS D 212 " pdb=" CB LYS D 212 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA GLN D 917 " pdb=" N GLN D 917 " pdb=" C GLN D 917 " pdb=" CB GLN D 917 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA GLU D 205 " pdb=" N GLU D 205 " pdb=" C GLU D 205 " pdb=" CB GLU D 205 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 5214 not shown) Planarity restraints: 5344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS S 191 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS S 191 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS S 191 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA S 192 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 167 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C SER C 167 " 0.038 2.00e-02 2.50e+03 pdb=" O SER C 167 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU C 168 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 500 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ALA Z 500 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA Z 500 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN Z 501 " 0.012 2.00e-02 2.50e+03 ... (remaining 5341 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 202 2.44 - 3.06: 23011 3.06 - 3.67: 49860 3.67 - 4.29: 67954 4.29 - 4.90: 111024 Nonbonded interactions: 252051 Sorted by model distance: nonbonded pdb=" N2 DG G 6 " pdb=" O2 DC H 37 " model vdw 1.825 2.496 nonbonded pdb=" O ASN M 25 " pdb=" ND2 ASN M 25 " model vdw 1.869 2.520 nonbonded pdb=" OG1 THR S 8 " pdb=" OG SER S 15 " model vdw 1.908 2.440 nonbonded pdb=" C2' DT G 49 " pdb=" C5' DT G 50 " model vdw 1.944 3.840 nonbonded pdb=" N GLU C1286 " pdb=" OE1 GLU C1286 " model vdw 2.015 2.520 ... (remaining 252046 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 'K' selection = chain 'L' } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.040 Extract box with map and model: 10.870 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 93.610 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 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 0.215 32625 Z= 0.858 Angle : 1.537 11.312 44619 Z= 1.186 Chirality : 0.111 0.384 5217 Planarity : 0.005 0.032 5344 Dihedral : 15.193 173.721 12384 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 58.99 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.26 % Favored : 96.12 % Rotamer: Outliers : 5.14 % Allowed : 9.91 % Favored : 84.95 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.59 % 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: 3.17 (0.14), residues: 3713 helix: 4.48 (0.12), residues: 1537 sheet: 1.72 (0.26), residues: 376 loop : -0.00 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 234 HIS 0.004 0.001 HIS C1256 PHE 0.014 0.001 PHE S 75 TYR 0.014 0.002 TYR C1243 ARG 0.005 0.001 ARG Z 249 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 554 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7621 (mm-30) REVERT: C 8 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8125 (mmtm) REVERT: C 60 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.6901 (m-10) REVERT: C 188 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7404 (t80) REVERT: C 739 VAL cc_start: 0.7361 (OUTLIER) cc_final: 0.6384 (m) REVERT: D 16 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: D 55 PHE cc_start: 0.7471 (m-80) cc_final: 0.6934 (m-80) REVERT: D 374 LEU cc_start: 0.8865 (mt) cc_final: 0.7416 (mt) REVERT: D 620 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.4646 (m-30) REVERT: D 797 LEU cc_start: 0.8991 (mt) cc_final: 0.8674 (tp) REVERT: D 844 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: D 1231 MET cc_start: 0.8846 (ptt) cc_final: 0.8622 (ppp) REVERT: D 1256 ASP cc_start: 0.6406 (OUTLIER) cc_final: 0.5723 (p0) REVERT: D 1338 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7963 (m-40) REVERT: M 103 PHE cc_start: 0.6917 (m-80) cc_final: 0.6705 (m-80) REVERT: M 133 SER cc_start: 0.7218 (p) cc_final: 0.6991 (p) REVERT: S 15 SER cc_start: 0.7997 (t) cc_final: 0.7704 (m) REVERT: S 88 ARG cc_start: 0.6369 (ttm170) cc_final: 0.6004 (ttt90) REVERT: S 107 ASP cc_start: 0.8575 (m-30) cc_final: 0.7909 (m-30) REVERT: S 122 MET cc_start: 0.3476 (OUTLIER) cc_final: 0.3221 (mmp) REVERT: S 179 TYR cc_start: 0.7415 (p90) cc_final: 0.7136 (p90) REVERT: Z 125 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7983 (tp) REVERT: Z 443 THR cc_start: 0.6908 (OUTLIER) cc_final: 0.6428 (t) REVERT: Z 505 LEU cc_start: 0.8704 (tt) cc_final: 0.8483 (tt) outliers start: 156 outliers final: 39 residues processed: 684 average time/residue: 0.4919 time to fit residues: 521.7635 Evaluate side-chains 353 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 302 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 310 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 359 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 ASN C 138 ASN C 144 ASN C 466 GLN C 557 HIS C 621 GLN C 717 ASN C 810 ASN C1084 HIS C1130 HIS C1268 GLN C1319 ASN C1328 ASN C1336 ASN D 111 HIS ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN D 467 HIS D 553 GLN D 563 ASN D 863 ASN ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1240 HIS ** D1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN M 182 ASN ** Z 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 436 GLN ** Z 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32625 Z= 0.269 Angle : 0.739 13.685 44619 Z= 0.402 Chirality : 0.046 0.270 5217 Planarity : 0.005 0.047 5344 Dihedral : 15.274 179.329 5487 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.67 % Favored : 97.06 % Rotamer: Outliers : 0.33 % Allowed : 4.12 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: 1.27 (0.14), residues: 3713 helix: 2.22 (0.13), residues: 1596 sheet: 0.98 (0.26), residues: 400 loop : -0.52 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 809 HIS 0.012 0.002 HIS C1256 PHE 0.031 0.002 PHE C1277 TYR 0.040 0.002 TYR Z 242 ARG 0.025 0.001 ARG C 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 366 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8322 (pt0) REVERT: B 193 LEU cc_start: 0.7085 (tt) cc_final: 0.6855 (tt) REVERT: B 195 LEU cc_start: 0.7693 (tp) cc_final: 0.7428 (tp) REVERT: C 491 MET cc_start: 0.6538 (tpt) cc_final: 0.6252 (tpp) REVERT: M 19 LEU cc_start: 0.8388 (mt) cc_final: 0.8164 (mt) REVERT: M 97 GLU cc_start: 0.7167 (tt0) cc_final: 0.6866 (pt0) REVERT: M 103 PHE cc_start: 0.6535 (m-80) cc_final: 0.5647 (m-80) REVERT: M 109 LYS cc_start: 0.8863 (tmmt) cc_final: 0.8423 (ptmt) REVERT: S 179 TYR cc_start: 0.7032 (p90) cc_final: 0.6701 (p90) REVERT: Z 90 MET cc_start: 0.7252 (mtp) cc_final: 0.6581 (mtp) REVERT: Z 282 GLU cc_start: 0.8629 (pm20) cc_final: 0.8414 (pm20) REVERT: Z 510 LYS cc_start: 0.8838 (pptt) cc_final: 0.8561 (ptpp) REVERT: Z 533 MET cc_start: 0.5106 (mmt) cc_final: 0.4663 (ptm) outliers start: 10 outliers final: 5 residues processed: 373 average time/residue: 0.4836 time to fit residues: 280.6400 Evaluate side-chains 263 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 258 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 299 optimal weight: 50.0000 chunk 244 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 360 optimal weight: 30.0000 chunk 389 optimal weight: 4.9990 chunk 320 optimal weight: 30.0000 chunk 357 optimal weight: 0.1980 chunk 122 optimal weight: 0.8980 chunk 289 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 ASN C 89 GLN C 529 HIS ** C1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1338 ASN ** M 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 324 GLN Z 338 GLN Z 370 GLN Z 373 ASN ** Z 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 566 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32625 Z= 0.215 Angle : 0.647 11.351 44619 Z= 0.354 Chirality : 0.044 0.544 5217 Planarity : 0.004 0.097 5344 Dihedral : 15.874 179.313 5487 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 0.13 % Allowed : 4.51 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.69 (0.13), residues: 3713 helix: 1.68 (0.13), residues: 1612 sheet: 0.59 (0.25), residues: 393 loop : -0.78 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 102 HIS 0.005 0.001 HIS C 800 PHE 0.036 0.002 PHE M 166 TYR 0.021 0.002 TYR D 624 ARG 0.017 0.001 ARG S 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 314 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 57 GLU cc_start: 0.7508 (pt0) cc_final: 0.7179 (mm-30) REVERT: D 483 MET cc_start: 0.6569 (tpt) cc_final: 0.6116 (tpt) REVERT: D 695 MET cc_start: 0.8174 (ppp) cc_final: 0.7423 (ppp) REVERT: D 734 MET cc_start: 0.8413 (ppp) cc_final: 0.8001 (ppp) REVERT: M 19 LEU cc_start: 0.8546 (mt) cc_final: 0.8285 (mt) REVERT: M 97 GLU cc_start: 0.7485 (tt0) cc_final: 0.6414 (pp20) REVERT: M 193 GLU cc_start: 0.7551 (tp30) cc_final: 0.7269 (tp30) REVERT: S 27 MET cc_start: 0.4920 (tmm) cc_final: 0.4661 (tmm) REVERT: S 55 MET cc_start: 0.5444 (mmp) cc_final: 0.4494 (mmm) REVERT: S 179 TYR cc_start: 0.7050 (p90) cc_final: 0.6500 (p90) REVERT: Z 125 LEU cc_start: 0.8532 (tp) cc_final: 0.8213 (pp) REVERT: Z 316 MET cc_start: 0.6364 (mmt) cc_final: 0.5130 (mmt) outliers start: 4 outliers final: 2 residues processed: 317 average time/residue: 0.4773 time to fit residues: 236.7705 Evaluate side-chains 236 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 chunk 39 optimal weight: 0.0770 chunk 171 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 382 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 overall best weight: 2.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32625 Z= 0.219 Angle : 0.609 9.915 44619 Z= 0.335 Chirality : 0.042 0.255 5217 Planarity : 0.004 0.063 5344 Dihedral : 15.938 177.290 5487 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.44 (0.13), residues: 3713 helix: 1.46 (0.13), residues: 1609 sheet: 0.46 (0.26), residues: 383 loop : -0.89 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 809 HIS 0.007 0.001 HIS Z 419 PHE 0.027 0.002 PHE D1262 TYR 0.023 0.001 TYR A 69 ARG 0.009 0.000 ARG S 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1080 MET cc_start: 0.7154 (tpt) cc_final: 0.6816 (tpt) REVERT: D 483 MET cc_start: 0.6676 (tpt) cc_final: 0.6195 (tpt) REVERT: M 19 LEU cc_start: 0.8545 (mt) cc_final: 0.8231 (mt) REVERT: M 70 GLU cc_start: 0.7586 (tp30) cc_final: 0.6346 (tp30) REVERT: M 74 ASP cc_start: 0.6869 (p0) cc_final: 0.6273 (p0) REVERT: M 97 GLU cc_start: 0.7366 (tt0) cc_final: 0.6534 (pp20) REVERT: M 193 GLU cc_start: 0.7563 (tp30) cc_final: 0.7295 (tp30) REVERT: S 55 MET cc_start: 0.5875 (mmp) cc_final: 0.4325 (tpt) REVERT: S 179 TYR cc_start: 0.7174 (p90) cc_final: 0.6863 (p90) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.4859 time to fit residues: 230.5658 Evaluate side-chains 229 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 285 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 326 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 343 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 ASN C1319 ASN D 33 HIS D 388 HIS ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32625 Z= 0.219 Angle : 0.606 13.834 44619 Z= 0.331 Chirality : 0.041 0.251 5217 Planarity : 0.005 0.180 5344 Dihedral : 16.082 179.599 5487 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.31 (0.14), residues: 3713 helix: 1.40 (0.13), residues: 1621 sheet: 0.16 (0.25), residues: 392 loop : -0.95 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Z 283 HIS 0.006 0.001 HIS C 800 PHE 0.050 0.002 PHE M 82 TYR 0.018 0.002 TYR C1241 ARG 0.035 0.001 ARG M 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 VAL cc_start: 0.5828 (p) cc_final: 0.4017 (p) REVERT: D 178 MET cc_start: 0.8047 (mtp) cc_final: 0.7622 (mtm) REVERT: D 483 MET cc_start: 0.6919 (tpt) cc_final: 0.6444 (tpt) REVERT: D 695 MET cc_start: 0.8133 (ppp) cc_final: 0.7585 (ppp) REVERT: D 696 MET cc_start: 0.7586 (mmt) cc_final: 0.7310 (mmm) REVERT: D 734 MET cc_start: 0.8420 (ppp) cc_final: 0.8189 (ppp) REVERT: D 1297 ILE cc_start: 0.8830 (pt) cc_final: 0.8585 (pt) REVERT: M 70 GLU cc_start: 0.7707 (tp30) cc_final: 0.6915 (tp30) REVERT: M 74 ASP cc_start: 0.6799 (p0) cc_final: 0.6485 (p0) REVERT: M 97 GLU cc_start: 0.7438 (tt0) cc_final: 0.6653 (pp20) REVERT: M 193 GLU cc_start: 0.7655 (tp30) cc_final: 0.7363 (tp30) REVERT: S 19 ARG cc_start: 0.3715 (ptt90) cc_final: 0.2502 (ptt180) REVERT: S 27 MET cc_start: 0.5575 (tmm) cc_final: 0.4273 (mmt) REVERT: S 55 MET cc_start: 0.5889 (mmp) cc_final: 0.5336 (mmm) REVERT: S 179 TYR cc_start: 0.7267 (p90) cc_final: 0.6926 (p90) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.4690 time to fit residues: 208.2510 Evaluate side-chains 213 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 0.7980 chunk 344 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 383 optimal weight: 0.1980 chunk 318 optimal weight: 0.3980 chunk 177 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 211 GLN ** Z 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32625 Z= 0.169 Angle : 0.571 8.556 44619 Z= 0.311 Chirality : 0.040 0.229 5217 Planarity : 0.004 0.076 5344 Dihedral : 16.073 177.511 5487 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.26 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.29 (0.14), residues: 3713 helix: 1.38 (0.13), residues: 1614 sheet: 0.12 (0.25), residues: 393 loop : -0.96 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 283 HIS 0.004 0.001 HIS C 800 PHE 0.032 0.001 PHE M 166 TYR 0.028 0.001 TYR C 3 ARG 0.008 0.000 ARG S 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 VAL cc_start: 0.5723 (p) cc_final: 0.3806 (p) REVERT: C 1318 LYS cc_start: 0.9193 (pttp) cc_final: 0.8977 (mmtp) REVERT: D 178 MET cc_start: 0.7905 (mtp) cc_final: 0.7615 (mtp) REVERT: D 483 MET cc_start: 0.6777 (tpt) cc_final: 0.6395 (tpt) REVERT: D 1297 ILE cc_start: 0.8800 (pt) cc_final: 0.8586 (pt) REVERT: M 74 ASP cc_start: 0.6745 (p0) cc_final: 0.6413 (p0) REVERT: M 103 PHE cc_start: 0.7209 (m-10) cc_final: 0.6145 (m-80) REVERT: M 193 GLU cc_start: 0.7706 (tp30) cc_final: 0.7429 (tp30) REVERT: S 27 MET cc_start: 0.5757 (tmm) cc_final: 0.5431 (tmm) REVERT: S 55 MET cc_start: 0.5903 (mmp) cc_final: 0.5333 (mmm) REVERT: S 179 TYR cc_start: 0.7208 (p90) cc_final: 0.6735 (p90) REVERT: Z 95 MET cc_start: 0.6389 (ppp) cc_final: 0.6158 (ppp) REVERT: Z 533 MET cc_start: 0.4978 (ptm) cc_final: 0.3251 (tmm) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.4702 time to fit residues: 207.4214 Evaluate side-chains 215 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 322 optimal weight: 20.0000 chunk 213 optimal weight: 0.5980 chunk 381 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 211 GLN ** Z 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32625 Z= 0.206 Angle : 0.593 8.684 44619 Z= 0.325 Chirality : 0.040 0.264 5217 Planarity : 0.004 0.070 5344 Dihedral : 16.307 178.015 5487 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.90 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: 0.17 (0.14), residues: 3713 helix: 1.29 (0.13), residues: 1610 sheet: 0.03 (0.25), residues: 385 loop : -1.02 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 102 HIS 0.006 0.001 HIS C 800 PHE 0.018 0.002 PHE M 166 TYR 0.025 0.001 TYR A 69 ARG 0.010 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 VAL cc_start: 0.6369 (p) cc_final: 0.4701 (p) REVERT: C 1327 MET cc_start: 0.7108 (ppp) cc_final: 0.6725 (ptp) REVERT: D 178 MET cc_start: 0.8028 (mtp) cc_final: 0.7730 (mtp) REVERT: D 483 MET cc_start: 0.6864 (tpt) cc_final: 0.6441 (tpt) REVERT: D 1295 MET cc_start: 0.8108 (mpp) cc_final: 0.7208 (mpp) REVERT: D 1297 ILE cc_start: 0.8915 (pt) cc_final: 0.8672 (pt) REVERT: M 74 ASP cc_start: 0.6779 (p0) cc_final: 0.6382 (p0) REVERT: M 97 GLU cc_start: 0.7459 (pt0) cc_final: 0.6256 (pp20) REVERT: M 103 PHE cc_start: 0.7183 (m-10) cc_final: 0.6752 (m-80) REVERT: M 193 GLU cc_start: 0.7840 (tp30) cc_final: 0.7539 (tp30) REVERT: S 27 MET cc_start: 0.5836 (tmm) cc_final: 0.4499 (mmt) REVERT: S 55 MET cc_start: 0.6063 (mmp) cc_final: 0.5420 (mmm) REVERT: S 87 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7965 (mm-30) REVERT: S 179 TYR cc_start: 0.7466 (p90) cc_final: 0.7006 (p90) REVERT: Z 95 MET cc_start: 0.6503 (ppp) cc_final: 0.6291 (ppp) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.4524 time to fit residues: 194.4235 Evaluate side-chains 210 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 300 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 874 HIS ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1291 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 HIS Z 326 ASN ** Z 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.8423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 32625 Z= 0.435 Angle : 0.868 16.854 44619 Z= 0.464 Chirality : 0.047 0.208 5217 Planarity : 0.006 0.083 5344 Dihedral : 16.979 177.790 5487 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 31.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.38 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.96 (0.13), residues: 3713 helix: 0.12 (0.12), residues: 1625 sheet: -0.50 (0.25), residues: 366 loop : -1.35 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 195 HIS 0.012 0.003 HIS D 388 PHE 0.046 0.004 PHE M 164 TYR 0.038 0.004 TYR C 3 ARG 0.012 0.001 ARG D1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 VAL cc_start: 0.7197 (p) cc_final: 0.6290 (t) REVERT: B 195 LEU cc_start: 0.8801 (tp) cc_final: 0.8599 (tp) REVERT: D 178 MET cc_start: 0.8364 (mtp) cc_final: 0.8040 (mtm) REVERT: D 483 MET cc_start: 0.8032 (tpt) cc_final: 0.7825 (tpp) REVERT: D 695 MET cc_start: 0.8886 (ppp) cc_final: 0.8446 (ppp) REVERT: D 696 MET cc_start: 0.7681 (mmt) cc_final: 0.7277 (mmm) REVERT: D 721 MET cc_start: 0.8991 (mtm) cc_final: 0.8471 (mpp) REVERT: M 66 SER cc_start: 0.7768 (m) cc_final: 0.7415 (p) REVERT: M 97 GLU cc_start: 0.7827 (pt0) cc_final: 0.6758 (pp20) REVERT: M 196 PHE cc_start: 0.7241 (t80) cc_final: 0.6189 (t80) REVERT: S 19 ARG cc_start: 0.4737 (ptt90) cc_final: 0.3510 (ptt180) REVERT: S 37 LEU cc_start: 0.7173 (mp) cc_final: 0.6743 (mp) REVERT: Z 95 MET cc_start: 0.6890 (ppp) cc_final: 0.6683 (ppp) REVERT: Z 533 MET cc_start: 0.5924 (ptm) cc_final: 0.4701 (tmm) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.4545 time to fit residues: 173.7025 Evaluate side-chains 191 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 355 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 321 optimal weight: 1.9990 chunk 336 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 HIS ** Z 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.8514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32625 Z= 0.212 Angle : 0.623 9.548 44619 Z= 0.340 Chirality : 0.041 0.204 5217 Planarity : 0.004 0.075 5344 Dihedral : 16.833 178.380 5487 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.63 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.45 (0.13), residues: 3713 helix: 0.75 (0.13), residues: 1602 sheet: -0.56 (0.24), residues: 411 loop : -1.22 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 183 HIS 0.012 0.001 HIS Z 419 PHE 0.021 0.002 PHE S 123 TYR 0.023 0.002 TYR D 73 ARG 0.021 0.001 ARG S 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 LEU cc_start: 0.8738 (tp) cc_final: 0.8465 (tp) REVERT: C 684 MET cc_start: 0.8380 (ptp) cc_final: 0.8054 (ptp) REVERT: D 178 MET cc_start: 0.8313 (mtp) cc_final: 0.8036 (mtm) REVERT: D 483 MET cc_start: 0.7721 (tpt) cc_final: 0.7513 (tpp) REVERT: D 695 MET cc_start: 0.8686 (ppp) cc_final: 0.8257 (ppp) REVERT: D 696 MET cc_start: 0.7667 (mmt) cc_final: 0.7217 (mmm) REVERT: D 721 MET cc_start: 0.8902 (mtm) cc_final: 0.8636 (mpp) REVERT: D 1295 MET cc_start: 0.8703 (pmm) cc_final: 0.8235 (pmm) REVERT: D 1335 LEU cc_start: 0.8329 (mp) cc_final: 0.7575 (pt) REVERT: M 30 ASP cc_start: 0.4988 (m-30) cc_final: 0.4283 (p0) REVERT: M 63 TYR cc_start: 0.6397 (p90) cc_final: 0.5018 (p90) REVERT: M 66 SER cc_start: 0.7686 (m) cc_final: 0.7311 (p) REVERT: M 74 ASP cc_start: 0.6949 (p0) cc_final: 0.6670 (p0) REVERT: M 97 GLU cc_start: 0.7929 (pt0) cc_final: 0.6745 (pp20) REVERT: S 19 ARG cc_start: 0.4513 (ptt90) cc_final: 0.3711 (ptt180) REVERT: Z 95 MET cc_start: 0.6774 (ppp) cc_final: 0.6566 (ppp) REVERT: Z 533 MET cc_start: 0.5704 (ptm) cc_final: 0.4711 (tmm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.4622 time to fit residues: 183.7957 Evaluate side-chains 197 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 5.9990 chunk 376 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 394 optimal weight: 10.0000 chunk 363 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 312 GLN ** Z 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.8861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32625 Z= 0.232 Angle : 0.636 10.476 44619 Z= 0.345 Chirality : 0.041 0.271 5217 Planarity : 0.004 0.071 5344 Dihedral : 16.867 179.813 5487 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.82 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.39 (0.13), residues: 3713 helix: 0.86 (0.13), residues: 1600 sheet: -0.52 (0.25), residues: 393 loop : -1.27 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 183 HIS 0.005 0.001 HIS D 448 PHE 0.025 0.002 PHE Z 546 TYR 0.033 0.002 TYR C1243 ARG 0.014 0.001 ARG Z 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 LEU cc_start: 0.8701 (tp) cc_final: 0.8452 (tp) REVERT: D 178 MET cc_start: 0.8286 (mtp) cc_final: 0.8023 (mtm) REVERT: D 695 MET cc_start: 0.8707 (ppp) cc_final: 0.8279 (ppp) REVERT: D 696 MET cc_start: 0.7670 (mmt) cc_final: 0.7253 (mmm) REVERT: D 721 MET cc_start: 0.8949 (mtm) cc_final: 0.8695 (mpp) REVERT: D 1295 MET cc_start: 0.8651 (pmm) cc_final: 0.7892 (pmm) REVERT: D 1335 LEU cc_start: 0.8362 (mp) cc_final: 0.7553 (pt) REVERT: M 30 ASP cc_start: 0.5459 (m-30) cc_final: 0.4800 (p0) REVERT: M 66 SER cc_start: 0.7942 (m) cc_final: 0.7577 (p) REVERT: M 74 ASP cc_start: 0.6942 (p0) cc_final: 0.6470 (p0) REVERT: M 97 GLU cc_start: 0.7910 (pt0) cc_final: 0.6812 (pp20) REVERT: M 133 SER cc_start: 0.8576 (p) cc_final: 0.8336 (p) REVERT: S 19 ARG cc_start: 0.4742 (ptt90) cc_final: 0.3961 (ptt180) REVERT: S 86 ASN cc_start: 0.7015 (m-40) cc_final: 0.6625 (m-40) REVERT: S 179 TYR cc_start: 0.7203 (p90) cc_final: 0.6371 (p90) REVERT: Z 125 LEU cc_start: 0.8319 (tp) cc_final: 0.7955 (pp) REVERT: Z 521 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6481 (mm-30) REVERT: Z 533 MET cc_start: 0.5719 (ptm) cc_final: 0.4897 (tmm) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.4670 time to fit residues: 182.3091 Evaluate side-chains 199 residues out of total 3269 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 6.9990 chunk 334 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 289 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 87 optimal weight: 0.3980 chunk 314 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 323 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 GLN ** C1328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** Z 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.055261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.038902 restraints weight = 344480.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.039703 restraints weight = 228745.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040214 restraints weight = 169445.878| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.9347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32625 Z= 0.247 Angle : 0.639 9.689 44619 Z= 0.348 Chirality : 0.041 0.233 5217 Planarity : 0.004 0.109 5344 Dihedral : 16.940 179.462 5487 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.03 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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 (0.14), residues: 3713 helix: 0.75 (0.13), residues: 1608 sheet: -0.66 (0.24), residues: 412 loop : -1.31 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 183 HIS 0.009 0.001 HIS D 362 PHE 0.030 0.002 PHE Z 546 TYR 0.030 0.002 TYR C1243 ARG 0.016 0.001 ARG M 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.78 seconds wall clock time: 109 minutes 45.17 seconds (6585.17 seconds total)