Starting phenix.real_space_refine on Fri Feb 23 09:28:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2k_11042/02_2024/6z2k_11042_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2k_11042/02_2024/6z2k_11042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2k_11042/02_2024/6z2k_11042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2k_11042/02_2024/6z2k_11042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2k_11042/02_2024/6z2k_11042_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2k_11042/02_2024/6z2k_11042_trim_updated.pdb" } resolution = 4.5 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 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: 8 Type Number sf(0) Gaussians K 8 8.98 5 Zn 4 6.06 5 P 24 5.49 5 S 122 5.16 5 C 12224 2.51 5 N 3262 2.21 5 O 3622 1.98 5 H 18577 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 18": "OD1" <-> "OD2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 18": "OD1" <-> "OD2" Residue "E TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 18": "OD1" <-> "OD2" Residue "I TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 771": "OD1" <-> "OD2" Residue "F PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 838": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 838": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 771": "OD1" <-> "OD2" Residue "L PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 838": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 771": "OD1" <-> "OD2" Residue "J PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 838": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37843 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5802 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5787 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5802 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5802 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Conformer: "B" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} bond proxies already assigned to first conformer: 1060 Chain: "B" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "G" Number of atoms: 1139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Conformer: "B" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} bond proxies already assigned to first conformer: 1060 Chain: "H" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2505 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' K': 2, ' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS A 121 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS A 121 " occ=0.50 residue: pdb=" N ACYS G 121 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS G 121 " occ=0.50 residue: pdb=" C1 IHP E 501 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP E 501 " occ=0.70 residue: pdb=" C1 IHP F 901 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP F 901 " occ=0.70 residue: pdb=" C1 IHP D 901 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP D 901 " occ=0.70 residue: pdb=" C1 IHP J 901 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP J 901 " occ=0.70 Time building chain proxies: 17.32, per 1000 atoms: 0.46 Number of scatterers: 37843 At special positions: 0 Unit cell: (137.16, 169.56, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 K 8 19.00 S 122 16.00 P 24 15.00 O 3622 8.00 N 3262 7.00 C 12224 6.00 H 18577 1.00 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: 31.95 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" ND1 HIS C 178 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 178 " pdb=" ZN I 501 " pdb="ZN ZN I 501 " - pdb=" ND1 HIS I 178 " pdb=" ZN K 501 " pdb="ZN ZN K 501 " - pdb=" ND1 HIS K 178 " 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 8 sheets defined 45.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 32 through 44 removed outlier: 4.137A pdb=" N LEU C 42 " --> pdb=" O HIS C 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 43 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 61 through 64 No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.707A pdb=" N ARG C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 125 removed outlier: 3.510A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.591A pdb=" N GLU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 234 through 251 Proline residue: C 243 - end of helix Processing helix chain 'C' and resid 278 through 291 removed outlier: 3.937A pdb=" N VAL C 285 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'E' and resid 17 through 20 Processing helix chain 'E' and resid 32 through 44 removed outlier: 4.138A pdb=" N LEU E 42 " --> pdb=" O HIS E 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 43 " --> pdb=" O ASN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 61 through 64 No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.706A pdb=" N ARG E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.509A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.591A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 187 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 234 through 251 Proline residue: E 243 - end of helix Processing helix chain 'E' and resid 278 through 291 removed outlier: 3.937A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 319 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'K' and resid 17 through 20 Processing helix chain 'K' and resid 32 through 44 removed outlier: 4.138A pdb=" N LEU K 42 " --> pdb=" O HIS K 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 43 " --> pdb=" O ASN K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 61 through 64 No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 70 through 78 Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.707A pdb=" N ARG K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 125 removed outlier: 3.510A pdb=" N SER K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 165 removed outlier: 3.591A pdb=" N GLU K 162 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS K 165 " --> pdb=" O LEU K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 Processing helix chain 'K' and resid 217 through 219 No H-bonds generated for 'chain 'K' and resid 217 through 219' Processing helix chain 'K' and resid 234 through 251 Proline residue: K 243 - end of helix Processing helix chain 'K' and resid 278 through 291 removed outlier: 3.937A pdb=" N VAL K 285 " --> pdb=" O HIS K 281 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE K 291 " --> pdb=" O PHE K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 319 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 356 through 372 Processing helix chain 'I' and resid 17 through 20 Processing helix chain 'I' and resid 32 through 44 removed outlier: 4.137A pdb=" N LEU I 42 " --> pdb=" O HIS I 39 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU I 43 " --> pdb=" O ASN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 61 through 64 No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.706A pdb=" N ARG I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 125 removed outlier: 3.511A pdb=" N SER I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 165 removed outlier: 3.591A pdb=" N GLU I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 187 Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 234 through 251 Proline residue: I 243 - end of helix Processing helix chain 'I' and resid 278 through 291 removed outlier: 3.937A pdb=" N VAL I 285 " --> pdb=" O HIS I 281 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE I 291 " --> pdb=" O PHE I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 305 through 319 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 356 through 372 Processing helix chain 'A' and resid 63 through 88 removed outlier: 3.597A pdb=" N LEU A 70 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 3.556A pdb=" N GLN A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.639A pdb=" N LYS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 88 removed outlier: 3.522A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.834A pdb=" N LYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 104 Processing helix chain 'B' and resid 110 through 129 removed outlier: 3.542A pdb=" N LYS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 88 removed outlier: 3.606A pdb=" N LEU G 70 " --> pdb=" O MET G 67 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG G 71 " --> pdb=" O ASP G 68 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN G 75 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Proline residue: G 76 - end of helix removed outlier: 3.514A pdb=" N ILE G 82 " --> pdb=" O ASN G 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE G 86 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN G 87 " --> pdb=" O THR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 103 Processing helix chain 'G' and resid 110 through 129 removed outlier: 3.528A pdb=" N LYS G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU G 127 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU G 128 " --> pdb=" O GLN G 124 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE G 129 " --> pdb=" O ALA G 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 88 Proline residue: H 76 - end of helix removed outlier: 3.817A pdb=" N LYS H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 104 Processing helix chain 'H' and resid 110 through 129 removed outlier: 3.608A pdb=" N LYS H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU H 128 " --> pdb=" O GLN H 124 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE H 129 " --> pdb=" O ALA H 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 766 through 774 removed outlier: 4.161A pdb=" N GLU F 770 " --> pdb=" O GLN F 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 798 Processing helix chain 'F' and resid 803 through 810 Processing helix chain 'F' and resid 823 through 828 Processing helix chain 'F' and resid 835 through 847 Processing helix chain 'F' and resid 854 through 858 Processing helix chain 'F' and resid 864 through 877 Processing helix chain 'D' and resid 766 through 774 removed outlier: 4.162A pdb=" N GLU D 770 " --> pdb=" O GLN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 798 Processing helix chain 'D' and resid 803 through 810 Processing helix chain 'D' and resid 823 through 828 Processing helix chain 'D' and resid 835 through 847 Processing helix chain 'D' and resid 854 through 858 Processing helix chain 'D' and resid 864 through 877 Processing helix chain 'L' and resid 766 through 774 removed outlier: 4.162A pdb=" N GLU L 770 " --> pdb=" O GLN L 766 " (cutoff:3.500A) Processing helix chain 'L' and resid 789 through 798 Processing helix chain 'L' and resid 803 through 810 Processing helix chain 'L' and resid 823 through 828 Processing helix chain 'L' and resid 835 through 847 Processing helix chain 'L' and resid 854 through 858 Processing helix chain 'L' and resid 864 through 877 Processing helix chain 'J' and resid 766 through 774 removed outlier: 4.161A pdb=" N GLU J 770 " --> pdb=" O GLN J 766 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 798 Processing helix chain 'J' and resid 803 through 810 Processing helix chain 'J' and resid 823 through 828 Processing helix chain 'J' and resid 835 through 847 Processing helix chain 'J' and resid 854 through 858 Processing helix chain 'J' and resid 864 through 877 Processing sheet with id= A, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.797A pdb=" N ILE C 131 " --> pdb=" O CYS C 12 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR C 14 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 133 " --> pdb=" O TYR C 14 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET C 295 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASN C 134 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET C 297 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 193 through 195 removed outlier: 7.016A pdb=" N VAL C 170 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA C 256 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 173 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 258 " --> pdb=" O ILE C 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'E' and resid 52 through 54 removed outlier: 6.797A pdb=" N ILE E 131 " --> pdb=" O CYS E 12 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N TYR E 14 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL E 133 " --> pdb=" O TYR E 14 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET E 295 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASN E 134 " --> pdb=" O MET E 295 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET E 297 " --> pdb=" O ASN E 134 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 193 through 195 removed outlier: 7.016A pdb=" N VAL E 170 " --> pdb=" O MET E 194 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA E 256 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE E 173 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 258 " --> pdb=" O ILE E 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'K' and resid 52 through 54 removed outlier: 6.797A pdb=" N ILE K 131 " --> pdb=" O CYS K 12 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N TYR K 14 " --> pdb=" O ILE K 131 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL K 133 " --> pdb=" O TYR K 14 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET K 295 " --> pdb=" O ALA K 132 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASN K 134 " --> pdb=" O MET K 295 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET K 297 " --> pdb=" O ASN K 134 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 193 through 195 removed outlier: 7.016A pdb=" N VAL K 170 " --> pdb=" O MET K 194 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA K 256 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE K 173 " --> pdb=" O ALA K 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL K 258 " --> pdb=" O ILE K 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'I' and resid 52 through 54 removed outlier: 6.797A pdb=" N ILE I 131 " --> pdb=" O CYS I 12 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR I 14 " --> pdb=" O ILE I 131 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL I 133 " --> pdb=" O TYR I 14 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET I 295 " --> pdb=" O ALA I 132 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASN I 134 " --> pdb=" O MET I 295 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N MET I 297 " --> pdb=" O ASN I 134 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 193 through 195 removed outlier: 7.017A pdb=" N VAL I 170 " --> pdb=" O MET I 194 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA I 256 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE I 173 " --> pdb=" O ALA I 256 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL I 258 " --> pdb=" O ILE I 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 637 hydrogen bonds defined for protein. 1709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.87 Time building geometry restraints manager: 33.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18523 1.03 - 1.23: 74 1.23 - 1.42: 8413 1.42 - 1.62: 11088 1.62 - 1.81: 194 Bond restraints: 38292 Sorted by residual: bond pdb=" O12 IHP F 901 " pdb=" P2 IHP F 901 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O12 IHP J 901 " pdb=" P2 IHP J 901 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O12 IHP E 501 " pdb=" P2 IHP E 501 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O12 IHP D 901 " pdb=" P2 IHP D 901 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O15 IHP D 901 " pdb=" P5 IHP D 901 " ideal model delta sigma weight residual 1.675 1.617 0.058 2.00e-02 2.50e+03 8.28e+00 ... (remaining 38287 not shown) Histogram of bond angle deviations from ideal: 95.10 - 102.88: 153 102.88 - 110.67: 38648 110.67 - 118.45: 12136 118.45 - 126.24: 17580 126.24 - 134.02: 468 Bond angle restraints: 68985 Sorted by residual: angle pdb=" C GLY D 785 " pdb=" N THR D 786 " pdb=" CA THR D 786 " ideal model delta sigma weight residual 121.33 129.53 -8.20 1.40e+00 5.10e-01 3.43e+01 angle pdb=" C GLY J 785 " pdb=" N THR J 786 " pdb=" CA THR J 786 " ideal model delta sigma weight residual 121.33 129.50 -8.17 1.40e+00 5.10e-01 3.40e+01 angle pdb=" C GLY F 785 " pdb=" N THR F 786 " pdb=" CA THR F 786 " ideal model delta sigma weight residual 121.33 129.49 -8.16 1.40e+00 5.10e-01 3.40e+01 angle pdb=" C GLY L 785 " pdb=" N THR L 786 " pdb=" CA THR L 786 " ideal model delta sigma weight residual 121.33 129.47 -8.14 1.40e+00 5.10e-01 3.38e+01 angle pdb=" CB LEU D 741 " pdb=" CG LEU D 741 " pdb=" HG LEU D 741 " ideal model delta sigma weight residual 109.00 95.94 13.06 3.00e+00 1.11e-01 1.90e+01 ... (remaining 68980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 17125 24.13 - 48.25: 868 48.25 - 72.38: 207 72.38 - 96.51: 23 96.51 - 120.63: 24 Dihedral angle restraints: 18247 sinusoidal: 9771 harmonic: 8476 Sorted by residual: dihedral pdb=" CA ASP J 745 " pdb=" C ASP J 745 " pdb=" N PRO J 746 " pdb=" CA PRO J 746 " ideal model delta harmonic sigma weight residual 180.00 116.60 63.40 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA ASP F 745 " pdb=" C ASP F 745 " pdb=" N PRO F 746 " pdb=" CA PRO F 746 " ideal model delta harmonic sigma weight residual 180.00 116.63 63.37 0 5.00e+00 4.00e-02 1.61e+02 dihedral pdb=" CA ASP D 745 " pdb=" C ASP D 745 " pdb=" N PRO D 746 " pdb=" CA PRO D 746 " ideal model delta harmonic sigma weight residual 180.00 116.68 63.32 0 5.00e+00 4.00e-02 1.60e+02 ... (remaining 18244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 2821 1.007 - 2.013: 4 2.013 - 3.020: 0 3.020 - 4.027: 0 4.027 - 5.033: 8 Chirality restraints: 2833 Sorted by residual: chirality pdb=" C2 IHP D 901 " pdb=" C1 IHP D 901 " pdb=" C3 IHP D 901 " pdb=" O12 IHP D 901 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP J 901 " pdb=" C1 IHP J 901 " pdb=" C3 IHP J 901 " pdb=" O12 IHP J 901 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP F 901 " pdb=" C1 IHP F 901 " pdb=" C3 IHP F 901 " pdb=" O12 IHP F 901 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 ... (remaining 2830 not shown) Planarity restraints: 5705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 745 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO D 746 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 746 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 746 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 745 " -0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO L 746 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO L 746 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO L 746 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 745 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO J 746 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO J 746 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO J 746 " 0.047 5.00e-02 4.00e+02 ... (remaining 5702 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.24: 4065 2.24 - 2.97: 102770 2.97 - 3.69: 141137 3.69 - 4.42: 215934 4.42 - 5.14: 334324 Nonbonded interactions: 798230 Sorted by model distance: nonbonded pdb=" HZ1 LYS F 843 " pdb=" O32 IHP F 901 " model vdw 1.518 1.850 nonbonded pdb=" O ARG E 49 " pdb=" HE1 TRP F 753 " model vdw 1.547 1.850 nonbonded pdb=" O ASN F 807 " pdb=" H LEU F 811 " model vdw 1.569 1.850 nonbonded pdb=" O ASN D 807 " pdb=" H LEU D 811 " model vdw 1.569 1.850 nonbonded pdb=" O ASN L 807 " pdb=" H LEU L 811 " model vdw 1.569 1.850 ... (remaining 798225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'B' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'G' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'H' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) } ncs_group { reference = (chain 'C' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 503)) selection = (chain 'E' and (resid 8 through 376 or resid 503)) selection = (chain 'I' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 503)) selection = (chain 'K' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 503)) } ncs_group { reference = (chain 'D' and resid 720 through 879) selection = (chain 'F' and resid 720 through 879) selection = (chain 'J' and resid 720 through 879) 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=0.50 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.590 Extract box with map and model: 14.850 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 135.810 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.006 0.069 19715 Z= 0.402 Angle : 0.994 12.261 26696 Z= 0.541 Chirality : 0.270 5.033 2833 Planarity : 0.005 0.086 3435 Dihedral : 16.147 120.634 7414 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.96 % Favored : 90.83 % Rotamer: Outliers : 0.15 % Allowed : 1.08 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.18 % 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: -3.76 (0.14), residues: 2355 helix: -2.01 (0.12), residues: 1130 sheet: -2.67 (0.34), residues: 200 loop : -2.95 (0.16), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 753 HIS 0.008 0.002 HIS F 796 PHE 0.022 0.002 PHE A 129 TYR 0.017 0.002 TYR E 303 ARG 0.009 0.001 ARG K 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 688 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 687 time to evaluate : 3.168 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: 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: 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: 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: C 18 ASP cc_start: 0.8695 (t0) cc_final: 0.8191 (t0) REVERT: C 47 LEU cc_start: 0.8784 (mt) cc_final: 0.8331 (mt) REVERT: C 110 CYS cc_start: 0.9467 (m) cc_final: 0.9245 (m) REVERT: C 242 LYS cc_start: 0.9266 (mttt) cc_final: 0.9057 (mtpp) REVERT: C 263 SER cc_start: 0.8471 (t) cc_final: 0.8162 (p) REVERT: C 284 CYS cc_start: 0.9011 (m) cc_final: 0.8503 (m) REVERT: E 18 ASP cc_start: 0.8691 (t0) cc_final: 0.8217 (t0) REVERT: E 47 LEU cc_start: 0.8870 (mt) cc_final: 0.8415 (mt) REVERT: E 110 CYS cc_start: 0.9411 (m) cc_final: 0.9179 (m) REVERT: E 242 LYS cc_start: 0.9267 (mttt) cc_final: 0.9047 (mtpp) REVERT: E 263 SER cc_start: 0.8542 (t) cc_final: 0.8320 (p) REVERT: E 367 PHE cc_start: 0.9355 (m-80) cc_final: 0.8762 (m-10) REVERT: K 18 ASP cc_start: 0.8595 (t0) cc_final: 0.8105 (t0) REVERT: K 47 LEU cc_start: 0.8617 (mt) cc_final: 0.8175 (mt) REVERT: K 110 CYS cc_start: 0.9483 (m) cc_final: 0.9266 (m) REVERT: K 242 LYS cc_start: 0.9239 (mttt) cc_final: 0.8927 (mtpp) REVERT: K 263 SER cc_start: 0.8572 (t) cc_final: 0.8366 (p) REVERT: K 367 PHE cc_start: 0.9366 (m-80) cc_final: 0.8764 (m-10) REVERT: I 18 ASP cc_start: 0.8624 (t0) cc_final: 0.8089 (t0) REVERT: I 47 LEU cc_start: 0.8969 (mt) cc_final: 0.8560 (mt) REVERT: I 110 CYS cc_start: 0.9420 (m) cc_final: 0.9196 (m) REVERT: I 242 LYS cc_start: 0.9328 (mttt) cc_final: 0.9077 (mtpp) REVERT: I 284 CYS cc_start: 0.9000 (m) cc_final: 0.8499 (m) REVERT: A 99 ASN cc_start: 0.8882 (m-40) cc_final: 0.8633 (t0) REVERT: B 65 ILE cc_start: 0.9018 (mm) cc_final: 0.8633 (tt) REVERT: H 65 ILE cc_start: 0.8996 (mm) cc_final: 0.8770 (tt) REVERT: F 757 GLU cc_start: 0.8978 (pt0) cc_final: 0.8685 (pp20) REVERT: F 801 ASP cc_start: 0.7790 (t70) cc_final: 0.6904 (m-30) REVERT: D 757 GLU cc_start: 0.9049 (pt0) cc_final: 0.8777 (pp20) REVERT: D 801 ASP cc_start: 0.8122 (t70) cc_final: 0.7681 (m-30) REVERT: D 874 TYR cc_start: 0.8672 (t80) cc_final: 0.8111 (t80) REVERT: L 757 GLU cc_start: 0.8790 (pt0) cc_final: 0.8581 (pp20) REVERT: L 801 ASP cc_start: 0.8179 (t70) cc_final: 0.7466 (m-30) REVERT: J 757 GLU cc_start: 0.8877 (pt0) cc_final: 0.8672 (pp20) REVERT: J 801 ASP cc_start: 0.8021 (t70) cc_final: 0.7460 (m-30) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.8211 time to fit residues: 826.5907 Evaluate side-chains 474 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 108 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 HIS ** F 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19715 Z= 0.225 Angle : 0.758 10.097 26696 Z= 0.386 Chirality : 0.045 0.427 2833 Planarity : 0.005 0.082 3435 Dihedral : 7.802 57.530 2792 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.61 % Favored : 91.22 % Rotamer: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.76 (0.16), residues: 2355 helix: -0.97 (0.14), residues: 1162 sheet: -2.51 (0.36), residues: 200 loop : -2.69 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 753 HIS 0.005 0.001 HIS K 167 PHE 0.020 0.002 PHE F 870 TYR 0.018 0.001 TYR C 358 ARG 0.011 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 559 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 3.088 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: 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: 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: 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 18 ASP cc_start: 0.8720 (t0) cc_final: 0.8274 (t0) REVERT: C 263 SER cc_start: 0.8553 (t) cc_final: 0.8194 (p) REVERT: C 296 LEU cc_start: 0.8948 (tp) cc_final: 0.8743 (tp) REVERT: E 18 ASP cc_start: 0.8851 (t0) cc_final: 0.8406 (t0) REVERT: E 242 LYS cc_start: 0.9295 (mttt) cc_final: 0.9007 (mmtt) REVERT: E 263 SER cc_start: 0.8728 (t) cc_final: 0.8245 (p) REVERT: E 296 LEU cc_start: 0.8897 (tp) cc_final: 0.8686 (tp) REVERT: K 18 ASP cc_start: 0.8664 (t0) cc_final: 0.8286 (t0) REVERT: K 296 LEU cc_start: 0.8908 (tp) cc_final: 0.8660 (tp) REVERT: I 18 ASP cc_start: 0.8746 (t0) cc_final: 0.8282 (t0) REVERT: I 315 GLU cc_start: 0.8833 (tt0) cc_final: 0.8447 (tt0) REVERT: G 99 ASN cc_start: 0.8989 (m-40) cc_final: 0.8517 (t0) REVERT: H 65 ILE cc_start: 0.9193 (mm) cc_final: 0.8983 (tt) REVERT: F 753 TRP cc_start: 0.8238 (t-100) cc_final: 0.8021 (t-100) REVERT: F 801 ASP cc_start: 0.7848 (t70) cc_final: 0.6911 (m-30) REVERT: F 835 MET cc_start: 0.8237 (pmm) cc_final: 0.7658 (tpp) REVERT: D 801 ASP cc_start: 0.8027 (t70) cc_final: 0.7351 (m-30) REVERT: D 841 PHE cc_start: 0.8046 (t80) cc_final: 0.7428 (t80) REVERT: D 868 VAL cc_start: 0.9459 (p) cc_final: 0.9189 (m) REVERT: D 874 TYR cc_start: 0.8580 (t80) cc_final: 0.8117 (t80) REVERT: L 801 ASP cc_start: 0.8064 (t70) cc_final: 0.7337 (m-30) REVERT: J 801 ASP cc_start: 0.7988 (t70) cc_final: 0.7232 (m-30) REVERT: J 876 LYS cc_start: 0.8430 (mttt) cc_final: 0.7832 (tptt) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.7749 time to fit residues: 640.8565 Evaluate side-chains 443 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN F 766 GLN ** F 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 GLN L 766 GLN J 766 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19715 Z= 0.289 Angle : 0.734 8.557 26696 Z= 0.391 Chirality : 0.041 0.262 2833 Planarity : 0.005 0.076 3435 Dihedral : 7.166 55.862 2792 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.11 % Favored : 89.72 % Rotamer: Outliers : 0.20 % Allowed : 3.15 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.76 (0.16), residues: 2355 helix: -0.91 (0.14), residues: 1166 sheet: -2.94 (0.35), residues: 212 loop : -2.67 (0.17), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 753 HIS 0.013 0.002 HIS D 796 PHE 0.022 0.002 PHE F 870 TYR 0.012 0.001 TYR C 358 ARG 0.016 0.001 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 527 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 525 time to evaluate : 3.093 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: 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: 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: 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 18 ASP cc_start: 0.8901 (t0) cc_final: 0.8498 (t0) REVERT: C 226 TYR cc_start: 0.7958 (t80) cc_final: 0.7739 (t80) REVERT: C 259 LEU cc_start: 0.8544 (tp) cc_final: 0.8337 (tp) REVERT: C 263 SER cc_start: 0.8828 (t) cc_final: 0.8351 (p) REVERT: C 296 LEU cc_start: 0.9149 (tp) cc_final: 0.8946 (tp) REVERT: E 18 ASP cc_start: 0.8933 (t0) cc_final: 0.8540 (t0) REVERT: E 172 TYR cc_start: 0.8459 (t80) cc_final: 0.8244 (t80) REVERT: E 242 LYS cc_start: 0.9405 (mttt) cc_final: 0.8993 (mmmt) REVERT: E 263 SER cc_start: 0.8586 (t) cc_final: 0.8251 (p) REVERT: K 18 ASP cc_start: 0.8883 (t0) cc_final: 0.8521 (t0) REVERT: K 242 LYS cc_start: 0.9419 (mttt) cc_final: 0.9001 (mmmt) REVERT: K 296 LEU cc_start: 0.9134 (tp) cc_final: 0.8923 (tp) REVERT: K 367 PHE cc_start: 0.9403 (m-80) cc_final: 0.8707 (m-10) REVERT: I 18 ASP cc_start: 0.8871 (t0) cc_final: 0.8421 (t0) REVERT: I 172 TYR cc_start: 0.8407 (t80) cc_final: 0.7953 (t80) REVERT: I 185 GLU cc_start: 0.9679 (mp0) cc_final: 0.9472 (mp0) REVERT: I 242 LYS cc_start: 0.9471 (mtpp) cc_final: 0.9228 (mtpp) REVERT: I 259 LEU cc_start: 0.8290 (tp) cc_final: 0.8053 (tp) REVERT: A 99 ASN cc_start: 0.9056 (m-40) cc_final: 0.8651 (t0) REVERT: B 116 GLU cc_start: 0.9349 (tp30) cc_final: 0.9148 (tp30) REVERT: G 99 ASN cc_start: 0.9061 (m-40) cc_final: 0.8611 (t0) REVERT: F 835 MET cc_start: 0.8247 (pmm) cc_final: 0.7613 (tpp) REVERT: D 801 ASP cc_start: 0.8162 (t70) cc_final: 0.7328 (m-30) REVERT: D 841 PHE cc_start: 0.8028 (t80) cc_final: 0.7635 (t80) REVERT: D 868 VAL cc_start: 0.9369 (p) cc_final: 0.9055 (m) REVERT: D 874 TYR cc_start: 0.8592 (t80) cc_final: 0.8053 (t80) REVERT: L 801 ASP cc_start: 0.8029 (t70) cc_final: 0.7048 (m-30) REVERT: L 841 PHE cc_start: 0.7963 (t80) cc_final: 0.7729 (t80) REVERT: J 801 ASP cc_start: 0.7886 (t70) cc_final: 0.6900 (m-30) outliers start: 2 outliers final: 1 residues processed: 527 average time/residue: 0.7705 time to fit residues: 611.4858 Evaluate side-chains 428 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.0000 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** F 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 GLN ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 766 GLN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 766 GLN ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19715 Z= 0.209 Angle : 0.659 8.125 26696 Z= 0.345 Chirality : 0.039 0.217 2833 Planarity : 0.005 0.074 3435 Dihedral : 6.786 54.620 2792 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.72 % Favored : 90.11 % Rotamer: Outliers : 0.10 % Allowed : 1.72 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.44 (0.16), residues: 2355 helix: -0.64 (0.15), residues: 1158 sheet: -2.87 (0.35), residues: 206 loop : -2.49 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 312 HIS 0.013 0.001 HIS L 796 PHE 0.016 0.002 PHE C 367 TYR 0.017 0.001 TYR E 333 ARG 0.007 0.001 ARG J 799 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 507 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 506 time to evaluate : 3.389 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.8913 (t0) cc_final: 0.8517 (t0) REVERT: C 172 TYR cc_start: 0.8378 (t80) cc_final: 0.7534 (t80) REVERT: C 263 SER cc_start: 0.8760 (t) cc_final: 0.8239 (p) REVERT: C 287 PHE cc_start: 0.9035 (t80) cc_final: 0.8603 (t80) REVERT: E 18 ASP cc_start: 0.8969 (t0) cc_final: 0.8571 (t0) REVERT: E 110 CYS cc_start: 0.9334 (m) cc_final: 0.9119 (m) REVERT: E 117 SER cc_start: 0.8582 (m) cc_final: 0.8377 (p) REVERT: E 242 LYS cc_start: 0.9395 (mttt) cc_final: 0.9013 (mmmt) REVERT: E 263 SER cc_start: 0.8732 (t) cc_final: 0.8289 (p) REVERT: E 287 PHE cc_start: 0.9040 (t80) cc_final: 0.8732 (t80) REVERT: E 296 LEU cc_start: 0.8893 (tp) cc_final: 0.8668 (tp) REVERT: K 18 ASP cc_start: 0.8891 (t0) cc_final: 0.8535 (t0) REVERT: K 172 TYR cc_start: 0.8276 (t80) cc_final: 0.7817 (t80) REVERT: K 242 LYS cc_start: 0.9436 (mttt) cc_final: 0.9034 (mmmt) REVERT: K 366 LEU cc_start: 0.9596 (tp) cc_final: 0.9376 (tp) REVERT: I 18 ASP cc_start: 0.8862 (t0) cc_final: 0.8418 (t0) REVERT: I 172 TYR cc_start: 0.8322 (t80) cc_final: 0.7890 (t80) REVERT: I 226 TYR cc_start: 0.7894 (t80) cc_final: 0.7669 (t80) REVERT: I 296 LEU cc_start: 0.8947 (tp) cc_final: 0.8736 (tp) REVERT: A 99 ASN cc_start: 0.9027 (m-40) cc_final: 0.8642 (t0) REVERT: B 65 ILE cc_start: 0.9177 (mm) cc_final: 0.8913 (tt) REVERT: B 116 GLU cc_start: 0.9368 (tp30) cc_final: 0.9154 (tp30) REVERT: G 67 MET cc_start: 0.9468 (mmm) cc_final: 0.9252 (mmm) REVERT: G 99 ASN cc_start: 0.9080 (m-40) cc_final: 0.8607 (t0) REVERT: H 108 VAL cc_start: 0.7754 (t) cc_final: 0.7453 (p) REVERT: F 835 MET cc_start: 0.8201 (pmm) cc_final: 0.7439 (tmm) REVERT: D 781 PHE cc_start: 0.5980 (p90) cc_final: 0.5696 (p90) REVERT: D 801 ASP cc_start: 0.8170 (t70) cc_final: 0.7258 (m-30) REVERT: D 841 PHE cc_start: 0.8044 (t80) cc_final: 0.7658 (t80) REVERT: D 868 VAL cc_start: 0.9410 (p) cc_final: 0.9103 (m) REVERT: L 781 PHE cc_start: 0.6233 (p90) cc_final: 0.5759 (p90) REVERT: L 801 ASP cc_start: 0.7983 (t70) cc_final: 0.7050 (m-30) REVERT: L 841 PHE cc_start: 0.7950 (t80) cc_final: 0.7449 (t80) REVERT: J 801 ASP cc_start: 0.7998 (t70) cc_final: 0.7003 (m-30) REVERT: J 841 PHE cc_start: 0.8174 (t80) cc_final: 0.7632 (t80) outliers start: 1 outliers final: 1 residues processed: 507 average time/residue: 0.7053 time to fit residues: 547.2764 Evaluate side-chains 421 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 420 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 0.0060 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 766 GLN ** F 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19715 Z= 0.196 Angle : 0.632 8.070 26696 Z= 0.333 Chirality : 0.038 0.186 2833 Planarity : 0.005 0.074 3435 Dihedral : 6.485 54.485 2792 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.89 % Favored : 89.94 % Rotamer: Outliers : 0.05 % Allowed : 1.43 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.23 (0.16), residues: 2355 helix: -0.42 (0.15), residues: 1157 sheet: -2.90 (0.35), residues: 206 loop : -2.41 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 753 HIS 0.006 0.001 HIS E 39 PHE 0.024 0.002 PHE I 334 TYR 0.025 0.001 TYR I 166 ARG 0.009 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 3.220 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: 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: 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: C 18 ASP cc_start: 0.8901 (t0) cc_final: 0.8468 (t0) REVERT: C 172 TYR cc_start: 0.8360 (t80) cc_final: 0.8015 (t80) REVERT: C 242 LYS cc_start: 0.9318 (mmtt) cc_final: 0.9084 (tptt) REVERT: C 259 LEU cc_start: 0.8297 (tp) cc_final: 0.8013 (tp) REVERT: C 263 SER cc_start: 0.8796 (t) cc_final: 0.8276 (p) REVERT: C 296 LEU cc_start: 0.8882 (tp) cc_final: 0.8650 (tp) REVERT: E 18 ASP cc_start: 0.8957 (t0) cc_final: 0.8564 (t0) REVERT: E 172 TYR cc_start: 0.8330 (t80) cc_final: 0.7954 (t80) REVERT: E 242 LYS cc_start: 0.9365 (mttt) cc_final: 0.8937 (mmmt) REVERT: E 259 LEU cc_start: 0.8283 (tp) cc_final: 0.7848 (tp) REVERT: E 263 SER cc_start: 0.8910 (t) cc_final: 0.8387 (p) REVERT: K 18 ASP cc_start: 0.8891 (t0) cc_final: 0.8546 (t0) REVERT: K 172 TYR cc_start: 0.8313 (t80) cc_final: 0.8029 (t80) REVERT: K 242 LYS cc_start: 0.9429 (mttt) cc_final: 0.9050 (mmmt) REVERT: I 18 ASP cc_start: 0.8890 (t0) cc_final: 0.8434 (t0) REVERT: I 296 LEU cc_start: 0.8998 (tp) cc_final: 0.8754 (tp) REVERT: A 99 ASN cc_start: 0.9049 (m-40) cc_final: 0.8499 (t0) REVERT: B 65 ILE cc_start: 0.9174 (mm) cc_final: 0.8912 (tt) REVERT: B 116 GLU cc_start: 0.9362 (tp30) cc_final: 0.9142 (tp30) REVERT: G 67 MET cc_start: 0.9511 (mmm) cc_final: 0.9291 (mmm) REVERT: G 99 ASN cc_start: 0.9102 (m-40) cc_final: 0.8633 (t0) REVERT: H 116 GLU cc_start: 0.9406 (tp30) cc_final: 0.9199 (tp30) REVERT: F 835 MET cc_start: 0.8099 (pmm) cc_final: 0.7333 (tmm) REVERT: D 801 ASP cc_start: 0.8150 (t70) cc_final: 0.7149 (m-30) REVERT: D 841 PHE cc_start: 0.8162 (t80) cc_final: 0.7807 (t80) REVERT: D 868 VAL cc_start: 0.9418 (p) cc_final: 0.9099 (m) REVERT: L 788 GLN cc_start: 0.7658 (pp30) cc_final: 0.7323 (pm20) REVERT: L 801 ASP cc_start: 0.8013 (t70) cc_final: 0.6996 (m-30) REVERT: L 841 PHE cc_start: 0.7794 (t80) cc_final: 0.7539 (t80) REVERT: J 801 ASP cc_start: 0.7973 (t70) cc_final: 0.6978 (m-30) REVERT: J 841 PHE cc_start: 0.8098 (t80) cc_final: 0.7742 (t80) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.7193 time to fit residues: 536.5032 Evaluate side-chains 413 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 766 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19715 Z= 0.297 Angle : 0.712 7.637 26696 Z= 0.384 Chirality : 0.040 0.158 2833 Planarity : 0.005 0.071 3435 Dihedral : 6.807 54.246 2792 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.20 % Favored : 87.63 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.65 (0.16), residues: 2355 helix: -0.84 (0.14), residues: 1173 sheet: -2.97 (0.35), residues: 196 loop : -2.58 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 312 HIS 0.009 0.002 HIS I 39 PHE 0.059 0.002 PHE H 129 TYR 0.022 0.002 TYR K 336 ARG 0.009 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 486 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 3.310 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: 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: 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: symmetry clash revert: symmetry clash REVERT: C 117 SER cc_start: 0.8715 (m) cc_final: 0.8477 (p) REVERT: C 172 TYR cc_start: 0.8486 (t80) cc_final: 0.8153 (t80) REVERT: C 226 TYR cc_start: 0.8160 (t80) cc_final: 0.7752 (t80) REVERT: C 242 LYS cc_start: 0.9388 (mmtt) cc_final: 0.9077 (mmmt) REVERT: C 259 LEU cc_start: 0.8399 (tp) cc_final: 0.8076 (tt) REVERT: C 263 SER cc_start: 0.8938 (t) cc_final: 0.8461 (p) REVERT: E 39 HIS cc_start: 0.9382 (t70) cc_final: 0.9055 (t70) REVERT: E 172 TYR cc_start: 0.8401 (t80) cc_final: 0.8029 (t80) REVERT: E 259 LEU cc_start: 0.8386 (tp) cc_final: 0.8142 (tt) REVERT: E 263 SER cc_start: 0.8911 (t) cc_final: 0.8426 (p) REVERT: E 296 LEU cc_start: 0.8695 (tp) cc_final: 0.8492 (tp) REVERT: E 372 MET cc_start: 0.9322 (tpp) cc_final: 0.9058 (tpp) REVERT: K 18 ASP cc_start: 0.9051 (t0) cc_final: 0.8806 (t0) REVERT: K 172 TYR cc_start: 0.8522 (t80) cc_final: 0.8289 (t80) REVERT: K 242 LYS cc_start: 0.9459 (mttt) cc_final: 0.9073 (mmmt) REVERT: K 259 LEU cc_start: 0.8507 (tp) cc_final: 0.8284 (tt) REVERT: I 172 TYR cc_start: 0.8576 (t80) cc_final: 0.8118 (t80) REVERT: I 296 LEU cc_start: 0.9005 (tp) cc_final: 0.8751 (tp) REVERT: A 99 ASN cc_start: 0.9106 (m-40) cc_final: 0.8683 (t0) REVERT: B 65 ILE cc_start: 0.9207 (mm) cc_final: 0.8942 (tt) REVERT: B 116 GLU cc_start: 0.9352 (tp30) cc_final: 0.9129 (tp30) REVERT: G 67 MET cc_start: 0.9517 (mmm) cc_final: 0.9299 (mmm) REVERT: G 99 ASN cc_start: 0.9119 (m-40) cc_final: 0.8635 (t0) REVERT: F 835 MET cc_start: 0.8130 (pmm) cc_final: 0.7249 (tmm) REVERT: D 781 PHE cc_start: 0.6067 (p90) cc_final: 0.5714 (p90) REVERT: D 839 LYS cc_start: 0.8523 (tptt) cc_final: 0.8260 (mmmt) REVERT: D 841 PHE cc_start: 0.8273 (t80) cc_final: 0.7901 (t80) REVERT: L 841 PHE cc_start: 0.7835 (t80) cc_final: 0.7575 (t80) REVERT: L 868 VAL cc_start: 0.9506 (m) cc_final: 0.9206 (m) REVERT: J 839 LYS cc_start: 0.8133 (tptt) cc_final: 0.7910 (mmmt) REVERT: J 841 PHE cc_start: 0.8185 (t80) cc_final: 0.7824 (t80) REVERT: J 868 VAL cc_start: 0.9567 (m) cc_final: 0.9354 (m) REVERT: J 872 TYR cc_start: 0.9467 (m-80) cc_final: 0.9230 (m-10) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.7218 time to fit residues: 528.6988 Evaluate side-chains 403 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 766 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19715 Z= 0.195 Angle : 0.620 9.951 26696 Z= 0.330 Chirality : 0.038 0.158 2833 Planarity : 0.004 0.070 3435 Dihedral : 6.628 54.121 2792 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.28 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.20 (0.16), residues: 2355 helix: -0.26 (0.15), residues: 1140 sheet: -2.95 (0.35), residues: 203 loop : -2.54 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 753 HIS 0.004 0.001 HIS J 793 PHE 0.081 0.002 PHE F 870 TYR 0.024 0.001 TYR F 874 ARG 0.006 0.001 ARG L 799 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 487 time to evaluate : 3.071 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: 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: 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: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.9065 (t0) cc_final: 0.8692 (t0) REVERT: C 39 HIS cc_start: 0.9356 (t70) cc_final: 0.9055 (t70) REVERT: C 172 TYR cc_start: 0.8510 (t80) cc_final: 0.8254 (t80) REVERT: C 226 TYR cc_start: 0.8158 (t80) cc_final: 0.7906 (t80) REVERT: C 242 LYS cc_start: 0.9514 (mmtt) cc_final: 0.9240 (mmmt) REVERT: C 259 LEU cc_start: 0.8437 (tp) cc_final: 0.8178 (tt) REVERT: C 263 SER cc_start: 0.8918 (t) cc_final: 0.8396 (p) REVERT: C 296 LEU cc_start: 0.8840 (tp) cc_final: 0.8628 (tp) REVERT: E 18 ASP cc_start: 0.9126 (t0) cc_final: 0.8791 (t0) REVERT: E 39 HIS cc_start: 0.9359 (t70) cc_final: 0.9037 (t70) REVERT: E 172 TYR cc_start: 0.8477 (t80) cc_final: 0.7582 (t80) REVERT: E 245 MET cc_start: 0.9439 (tpp) cc_final: 0.9226 (tpp) REVERT: E 259 LEU cc_start: 0.8372 (tp) cc_final: 0.8167 (tt) REVERT: E 263 SER cc_start: 0.8870 (t) cc_final: 0.8386 (p) REVERT: E 372 MET cc_start: 0.9255 (tpp) cc_final: 0.8998 (tpp) REVERT: K 18 ASP cc_start: 0.8948 (t0) cc_final: 0.8668 (t0) REVERT: K 296 LEU cc_start: 0.8841 (tp) cc_final: 0.8621 (tp) REVERT: I 259 LEU cc_start: 0.8237 (tp) cc_final: 0.8023 (tp) REVERT: I 296 LEU cc_start: 0.8973 (tp) cc_final: 0.8728 (tp) REVERT: A 82 ILE cc_start: 0.8735 (mt) cc_final: 0.8402 (mt) REVERT: A 99 ASN cc_start: 0.9116 (m-40) cc_final: 0.8709 (t0) REVERT: B 65 ILE cc_start: 0.9185 (mm) cc_final: 0.8925 (tt) REVERT: B 108 VAL cc_start: 0.7174 (t) cc_final: 0.6858 (p) REVERT: B 116 GLU cc_start: 0.9350 (tp30) cc_final: 0.9108 (tp30) REVERT: G 67 MET cc_start: 0.9502 (mmm) cc_final: 0.9287 (mmm) REVERT: G 99 ASN cc_start: 0.9114 (m-40) cc_final: 0.8604 (t0) REVERT: H 116 GLU cc_start: 0.9402 (tp30) cc_final: 0.9151 (tp30) REVERT: F 835 MET cc_start: 0.8065 (pmm) cc_final: 0.7145 (tmm) REVERT: D 781 PHE cc_start: 0.6229 (p90) cc_final: 0.5881 (p90) REVERT: D 839 LYS cc_start: 0.8405 (tptt) cc_final: 0.8148 (mmmt) REVERT: D 841 PHE cc_start: 0.8243 (t80) cc_final: 0.7862 (t80) REVERT: L 841 PHE cc_start: 0.7924 (t80) cc_final: 0.7600 (t80) REVERT: L 868 VAL cc_start: 0.9455 (m) cc_final: 0.9235 (m) REVERT: J 841 PHE cc_start: 0.8176 (t80) cc_final: 0.7814 (t80) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.6953 time to fit residues: 519.3305 Evaluate side-chains 404 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 139 optimal weight: 0.0870 chunk 149 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19715 Z= 0.173 Angle : 0.591 6.046 26696 Z= 0.314 Chirality : 0.038 0.156 2833 Planarity : 0.004 0.071 3435 Dihedral : 6.557 53.729 2792 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2355 helix: 0.13 (0.15), residues: 1133 sheet: -2.75 (0.37), residues: 203 loop : -2.37 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 753 HIS 0.008 0.001 HIS F 796 PHE 0.030 0.002 PHE F 870 TYR 0.021 0.001 TYR F 874 ARG 0.005 0.000 ARG L 799 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 479 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 3.089 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 ASP cc_start: 0.9024 (t0) cc_final: 0.8642 (t0) REVERT: C 39 HIS cc_start: 0.9376 (t70) cc_final: 0.9117 (t70) REVERT: C 172 TYR cc_start: 0.8505 (t80) cc_final: 0.8252 (t80) REVERT: C 226 TYR cc_start: 0.8267 (t80) cc_final: 0.7808 (t80) REVERT: C 242 LYS cc_start: 0.9441 (mmtt) cc_final: 0.9173 (mmmt) REVERT: C 259 LEU cc_start: 0.8394 (tp) cc_final: 0.8160 (tt) REVERT: C 263 SER cc_start: 0.8872 (t) cc_final: 0.8328 (p) REVERT: E 18 ASP cc_start: 0.9052 (t0) cc_final: 0.8658 (t70) REVERT: E 39 HIS cc_start: 0.9346 (t70) cc_final: 0.9044 (t70) REVERT: E 172 TYR cc_start: 0.8507 (t80) cc_final: 0.8233 (t80) REVERT: E 245 MET cc_start: 0.9434 (tpp) cc_final: 0.9221 (tpp) REVERT: E 248 VAL cc_start: 0.9594 (m) cc_final: 0.9350 (p) REVERT: E 263 SER cc_start: 0.8905 (t) cc_final: 0.8394 (p) REVERT: E 372 MET cc_start: 0.9237 (tpp) cc_final: 0.9002 (tpp) REVERT: K 18 ASP cc_start: 0.8881 (t0) cc_final: 0.8581 (t0) REVERT: K 296 LEU cc_start: 0.8790 (tp) cc_final: 0.8590 (tp) REVERT: I 18 ASP cc_start: 0.8980 (t0) cc_final: 0.8594 (t0) REVERT: I 172 TYR cc_start: 0.8612 (t80) cc_final: 0.8286 (t80) REVERT: I 296 LEU cc_start: 0.8946 (tp) cc_final: 0.8686 (tp) REVERT: A 82 ILE cc_start: 0.8723 (mt) cc_final: 0.8385 (mt) REVERT: A 99 ASN cc_start: 0.9123 (m-40) cc_final: 0.8710 (t0) REVERT: B 65 ILE cc_start: 0.9192 (mm) cc_final: 0.8843 (tt) REVERT: B 108 VAL cc_start: 0.7187 (t) cc_final: 0.6857 (p) REVERT: B 116 GLU cc_start: 0.9381 (tp30) cc_final: 0.9135 (tp30) REVERT: G 67 MET cc_start: 0.9495 (mmm) cc_final: 0.9266 (mmm) REVERT: G 99 ASN cc_start: 0.9104 (m-40) cc_final: 0.8586 (t0) REVERT: H 116 GLU cc_start: 0.9400 (tp30) cc_final: 0.9100 (tp30) REVERT: F 835 MET cc_start: 0.8053 (pmm) cc_final: 0.7180 (tmm) REVERT: D 839 LYS cc_start: 0.8367 (tptt) cc_final: 0.8121 (mmmt) REVERT: D 841 PHE cc_start: 0.8228 (t80) cc_final: 0.7842 (t80) REVERT: L 841 PHE cc_start: 0.7982 (t80) cc_final: 0.7637 (t80) REVERT: J 839 LYS cc_start: 0.8166 (tptt) cc_final: 0.7931 (mmmt) REVERT: J 841 PHE cc_start: 0.8274 (t80) cc_final: 0.7893 (t80) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.7100 time to fit residues: 527.5325 Evaluate side-chains 403 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 HIS I 39 HIS ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19715 Z= 0.264 Angle : 0.655 7.428 26696 Z= 0.356 Chirality : 0.039 0.207 2833 Planarity : 0.005 0.068 3435 Dihedral : 6.716 53.908 2792 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.90 % Favored : 87.93 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % 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: -2.20 (0.17), residues: 2355 helix: -0.38 (0.15), residues: 1164 sheet: -2.68 (0.40), residues: 188 loop : -2.51 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 753 HIS 0.017 0.002 HIS J 796 PHE 0.030 0.002 PHE F 841 TYR 0.017 0.002 TYR K 336 ARG 0.008 0.001 ARG D 799 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 3.271 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: 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: 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: C 172 TYR cc_start: 0.8602 (t80) cc_final: 0.7912 (t80) REVERT: C 229 ARG cc_start: 0.6219 (ptt180) cc_final: 0.5979 (ptt180) REVERT: C 245 MET cc_start: 0.9497 (tpp) cc_final: 0.9290 (tpp) REVERT: C 263 SER cc_start: 0.8923 (t) cc_final: 0.8420 (p) REVERT: E 39 HIS cc_start: 0.9394 (t70) cc_final: 0.9138 (t70) REVERT: E 172 TYR cc_start: 0.8590 (t80) cc_final: 0.8185 (t80) REVERT: E 241 PHE cc_start: 0.9317 (t80) cc_final: 0.9084 (t80) REVERT: E 242 LYS cc_start: 0.9386 (mttt) cc_final: 0.9138 (mmtt) REVERT: E 245 MET cc_start: 0.9514 (tpp) cc_final: 0.9311 (tpp) REVERT: E 263 SER cc_start: 0.8986 (t) cc_final: 0.8564 (p) REVERT: E 284 CYS cc_start: 0.9410 (m) cc_final: 0.8685 (m) REVERT: E 296 LEU cc_start: 0.8816 (tp) cc_final: 0.8604 (tp) REVERT: E 372 MET cc_start: 0.9320 (tpp) cc_final: 0.9106 (tpp) REVERT: K 18 ASP cc_start: 0.9113 (t0) cc_final: 0.8790 (t70) REVERT: K 39 HIS cc_start: 0.9326 (t70) cc_final: 0.9102 (t70) REVERT: K 172 TYR cc_start: 0.8515 (t80) cc_final: 0.7998 (t80) REVERT: K 296 LEU cc_start: 0.8836 (tp) cc_final: 0.8626 (tp) REVERT: K 372 MET cc_start: 0.9254 (tpt) cc_final: 0.8989 (tmm) REVERT: I 172 TYR cc_start: 0.8677 (t80) cc_final: 0.8239 (t80) REVERT: I 226 TYR cc_start: 0.8027 (t80) cc_final: 0.7718 (t80) REVERT: I 296 LEU cc_start: 0.8959 (tp) cc_final: 0.8704 (tp) REVERT: A 99 ASN cc_start: 0.9163 (m-40) cc_final: 0.8720 (t0) REVERT: B 65 ILE cc_start: 0.9226 (mm) cc_final: 0.8966 (tt) REVERT: B 108 VAL cc_start: 0.7219 (t) cc_final: 0.6922 (p) REVERT: B 116 GLU cc_start: 0.9389 (tp30) cc_final: 0.9183 (tp30) REVERT: G 67 MET cc_start: 0.9510 (mmm) cc_final: 0.9291 (mmm) REVERT: G 99 ASN cc_start: 0.9133 (m-40) cc_final: 0.8591 (t0) REVERT: H 116 GLU cc_start: 0.9412 (tp30) cc_final: 0.9168 (tp30) REVERT: F 835 MET cc_start: 0.8091 (pmm) cc_final: 0.7129 (tmm) REVERT: D 839 LYS cc_start: 0.8367 (tptt) cc_final: 0.8123 (mmmt) REVERT: D 841 PHE cc_start: 0.8211 (t80) cc_final: 0.7822 (t80) REVERT: D 868 VAL cc_start: 0.9515 (m) cc_final: 0.9314 (m) REVERT: D 872 TYR cc_start: 0.9227 (m-10) cc_final: 0.9025 (m-10) REVERT: L 781 PHE cc_start: 0.6376 (p90) cc_final: 0.5887 (p90) REVERT: L 809 LEU cc_start: 0.8607 (tt) cc_final: 0.8362 (tp) REVERT: L 841 PHE cc_start: 0.8102 (t80) cc_final: 0.7724 (t80) REVERT: L 868 VAL cc_start: 0.9479 (m) cc_final: 0.9253 (m) REVERT: J 839 LYS cc_start: 0.8191 (tptt) cc_final: 0.7941 (mmmt) REVERT: J 841 PHE cc_start: 0.8277 (t80) cc_final: 0.7877 (t80) REVERT: J 868 VAL cc_start: 0.9604 (m) cc_final: 0.9321 (m) REVERT: J 872 TYR cc_start: 0.9473 (m-80) cc_final: 0.9230 (m-10) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.6910 time to fit residues: 488.6463 Evaluate side-chains 390 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 227 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** L 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19715 Z= 0.174 Angle : 0.587 6.789 26696 Z= 0.312 Chirality : 0.037 0.153 2833 Planarity : 0.004 0.067 3435 Dihedral : 6.582 53.259 2792 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2355 helix: 0.17 (0.16), residues: 1133 sheet: -2.42 (0.40), residues: 188 loop : -2.44 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 753 HIS 0.009 0.001 HIS I 39 PHE 0.021 0.002 PHE I 103 TYR 0.016 0.001 TYR I 24 ARG 0.008 0.000 ARG D 799 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue ILE 733 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.062 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: 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: 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: C 18 ASP cc_start: 0.9100 (t0) cc_final: 0.8718 (t70) REVERT: C 175 ILE cc_start: 0.7845 (mm) cc_final: 0.7550 (tp) REVERT: C 245 MET cc_start: 0.9505 (tpp) cc_final: 0.9259 (tpp) REVERT: C 263 SER cc_start: 0.8833 (t) cc_final: 0.8343 (p) REVERT: E 18 ASP cc_start: 0.9135 (t0) cc_final: 0.8809 (t70) REVERT: E 172 TYR cc_start: 0.8544 (t80) cc_final: 0.8278 (t80) REVERT: E 226 TYR cc_start: 0.7994 (t80) cc_final: 0.7629 (t80) REVERT: E 245 MET cc_start: 0.9504 (tpp) cc_final: 0.9280 (tpp) REVERT: E 263 SER cc_start: 0.8819 (t) cc_final: 0.8340 (p) REVERT: E 296 LEU cc_start: 0.8715 (tp) cc_final: 0.8508 (tp) REVERT: E 372 MET cc_start: 0.9292 (tpp) cc_final: 0.9075 (tpp) REVERT: K 18 ASP cc_start: 0.8970 (t0) cc_final: 0.8619 (t70) REVERT: K 296 LEU cc_start: 0.8751 (tp) cc_final: 0.8534 (tp) REVERT: K 372 MET cc_start: 0.9246 (tpt) cc_final: 0.8999 (tmm) REVERT: I 18 ASP cc_start: 0.9103 (t0) cc_final: 0.8709 (t70) REVERT: I 172 TYR cc_start: 0.8665 (t80) cc_final: 0.8304 (t80) REVERT: I 226 TYR cc_start: 0.8215 (t80) cc_final: 0.7786 (t80) REVERT: I 259 LEU cc_start: 0.8299 (tp) cc_final: 0.8077 (tp) REVERT: I 296 LEU cc_start: 0.8908 (tp) cc_final: 0.8659 (tp) REVERT: A 82 ILE cc_start: 0.8701 (mt) cc_final: 0.8332 (mt) REVERT: A 99 ASN cc_start: 0.9157 (m-40) cc_final: 0.8672 (t0) REVERT: B 108 VAL cc_start: 0.7249 (t) cc_final: 0.6911 (p) REVERT: B 116 GLU cc_start: 0.9393 (tp30) cc_final: 0.9159 (tp30) REVERT: G 67 MET cc_start: 0.9500 (mmm) cc_final: 0.9282 (mmm) REVERT: G 99 ASN cc_start: 0.9114 (m-40) cc_final: 0.8547 (t0) REVERT: H 65 ILE cc_start: 0.9184 (mm) cc_final: 0.8973 (tt) REVERT: F 835 MET cc_start: 0.8072 (pmm) cc_final: 0.7133 (tmm) REVERT: D 839 LYS cc_start: 0.8400 (tptt) cc_final: 0.8144 (mmmt) REVERT: D 841 PHE cc_start: 0.8206 (t80) cc_final: 0.7844 (t80) REVERT: L 781 PHE cc_start: 0.6280 (p90) cc_final: 0.5861 (p90) REVERT: L 809 LEU cc_start: 0.8525 (tt) cc_final: 0.8297 (tp) REVERT: L 841 PHE cc_start: 0.8097 (t80) cc_final: 0.7713 (t80) REVERT: J 839 LYS cc_start: 0.8161 (tptt) cc_final: 0.7918 (mmmt) REVERT: J 841 PHE cc_start: 0.8270 (t80) cc_final: 0.7871 (t80) REVERT: J 872 TYR cc_start: 0.9453 (m-80) cc_final: 0.9217 (m-10) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.6749 time to fit residues: 482.0064 Evaluate side-chains 392 residues out of total 2063 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.096764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.076262 restraints weight = 368578.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.080665 restraints weight = 194258.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.083890 restraints weight = 120594.892| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3872 r_free = 0.3872 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19715 Z= 0.223 Angle : 0.602 6.082 26696 Z= 0.325 Chirality : 0.037 0.139 2833 Planarity : 0.005 0.066 3435 Dihedral : 6.597 53.605 2792 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.17), residues: 2355 helix: 0.08 (0.16), residues: 1120 sheet: -2.68 (0.37), residues: 203 loop : -2.40 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 753 HIS 0.008 0.001 HIS I 39 PHE 0.023 0.002 PHE C 103 TYR 0.019 0.001 TYR C 24 ARG 0.009 0.001 ARG D 799 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10457.31 seconds wall clock time: 185 minutes 36.54 seconds (11136.54 seconds total)