Starting phenix.real_space_refine on Sat Feb 17 13:37:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/02_2024/6z2j_11041_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/02_2024/6z2j_11041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/02_2024/6z2j_11041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/02_2024/6z2j_11041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/02_2024/6z2j_11041_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/02_2024/6z2j_11041_trim_updated.pdb" } resolution = 4.0 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= 0.002 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 4 8.98 5 Zn 2 6.06 5 P 12 5.49 5 S 61 5.16 5 C 6096 2.51 5 N 1626 2.21 5 O 1802 1.98 5 H 9273 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "E TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 233": "OD1" <-> "OD2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 763": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 770": "OE1" <-> "OE2" Residue "F ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 770": "OE1" <-> "OE2" Residue "D ARG 799": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 838": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18876 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5800 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: 5785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5785 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: "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: "F" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2488 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2488 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" 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: "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} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ACYS A 121 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS A 121 " occ=0.50 residue: pdb=" C1 IHP C 501 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP C 501 " occ=0.70 residue: pdb=" C1 IHP E 501 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP E 501 " occ=0.70 Time building chain proxies: 8.91, per 1000 atoms: 0.47 Number of scatterers: 18876 At special positions: 0 Unit cell: (149.04, 166.32, 69.12, 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 2 29.99 K 4 19.00 S 61 16.00 P 12 15.00 O 1802 8.00 N 1626 7.00 C 6096 6.00 H 9273 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: 13.63 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 178 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 178 " 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 4 sheets defined 46.0% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'C' and resid 18 through 21 removed outlier: 3.545A pdb=" N ASN C 21 " --> pdb=" O ASP C 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 32 through 44 Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 61 through 65 Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.640A pdb=" N LEU C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 106 through 125 removed outlier: 3.626A pdb=" N CYS C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 164 removed outlier: 4.204A pdb=" N GLU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 186 removed outlier: 3.857A pdb=" N ALA C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.804A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Proline residue: C 243 - end of helix removed outlier: 4.580A pdb=" N GLU C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 278 through 291 removed outlier: 3.561A pdb=" N CYS C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 285 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 320 removed outlier: 3.983A pdb=" N ALA C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) 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 removed outlier: 4.780A pdb=" N ILE C 362 " --> pdb=" O TYR C 358 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 21 removed outlier: 3.545A pdb=" N ASN E 21 " --> pdb=" O ASP E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 32 through 44 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.639A pdb=" N LEU E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 94 Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.626A pdb=" N CYS E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 113 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 164 removed outlier: 4.204A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 removed outlier: 3.857A pdb=" N ALA E 186 " --> pdb=" O GLY E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.804A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 4.580A pdb=" N GLU E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 265 No H-bonds generated for 'chain 'E' and resid 263 through 265' Processing helix chain 'E' and resid 278 through 291 removed outlier: 3.561A pdb=" N CYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 287 " --> pdb=" O LYS E 283 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 320 removed outlier: 3.983A pdb=" N ALA E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR E 314 " --> pdb=" O ARG E 310 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU E 320 " --> pdb=" O THR E 316 " (cutoff:3.500A) 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 removed outlier: 4.781A pdb=" N ILE E 362 " --> pdb=" O TYR E 358 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU E 368 " --> pdb=" O GLN E 364 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN E 369 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 103 removed outlier: 3.545A pdb=" N VAL A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 3.845A pdb=" N ASN A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 83 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 86 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 90 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 91 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A 94 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS A 95 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.754A pdb=" N ILE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 122 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 125 " --> pdb=" O ACYS A 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 104 removed outlier: 3.548A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.622A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 129 removed outlier: 3.529A pdb=" N ILE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 122 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 125 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 727 No H-bonds generated for 'chain 'F' and resid 725 through 727' Processing helix chain 'F' and resid 766 through 776 removed outlier: 3.502A pdb=" N GLU F 770 " --> pdb=" O GLN F 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 789 through 797 removed outlier: 4.116A pdb=" N HIS F 793 " --> pdb=" O GLU F 789 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS F 794 " --> pdb=" O LEU F 790 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS F 796 " --> pdb=" O LEU F 792 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU F 797 " --> pdb=" O HIS F 793 " (cutoff:3.500A) Processing helix chain 'F' and resid 803 through 809 removed outlier: 3.672A pdb=" N LYS F 808 " --> pdb=" O GLU F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 823 through 825 No H-bonds generated for 'chain 'F' and resid 823 through 825' Processing helix chain 'F' and resid 835 through 848 removed outlier: 3.926A pdb=" N ASN F 842 " --> pdb=" O ARG F 838 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA F 846 " --> pdb=" O ASN F 842 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE F 847 " --> pdb=" O LYS F 843 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 848 " --> pdb=" O GLY F 844 " (cutoff:3.500A) Processing helix chain 'F' and resid 854 through 858 Processing helix chain 'F' and resid 864 through 876 removed outlier: 3.713A pdb=" N PHE F 870 " --> pdb=" O GLN F 866 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR F 871 " --> pdb=" O CYS F 867 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 873 " --> pdb=" O GLU F 869 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 875 " --> pdb=" O TYR F 871 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N LYS F 876 " --> pdb=" O TYR F 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 766 through 776 removed outlier: 3.503A pdb=" N GLU D 770 " --> pdb=" O GLN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 797 removed outlier: 4.116A pdb=" N HIS D 793 " --> pdb=" O GLU D 789 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS D 794 " --> pdb=" O LEU D 790 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS D 796 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU D 797 " --> pdb=" O HIS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 809 removed outlier: 3.672A pdb=" N LYS D 808 " --> pdb=" O GLU D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 825 No H-bonds generated for 'chain 'D' and resid 823 through 825' Processing helix chain 'D' and resid 835 through 848 removed outlier: 3.926A pdb=" N ASN D 842 " --> pdb=" O ARG D 838 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 846 " --> pdb=" O ASN D 842 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE D 847 " --> pdb=" O LYS D 843 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 848 " --> pdb=" O GLY D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 858 Processing helix chain 'D' and resid 864 through 876 removed outlier: 3.713A pdb=" N PHE D 870 " --> pdb=" O GLN D 866 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR D 871 " --> pdb=" O CYS D 867 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 873 " --> pdb=" O GLU D 869 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 875 " --> pdb=" O TYR D 871 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS D 876 " --> pdb=" O TYR D 872 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 12 through 14 removed outlier: 5.965A pdb=" N GLU C 52 " --> pdb=" O TYR C 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.793A pdb=" N VAL C 170 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 256 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE C 173 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.702A 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 12 through 14 removed outlier: 5.964A pdb=" N GLU E 52 " --> pdb=" O TYR E 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.793A pdb=" N VAL E 170 " --> pdb=" O MET E 194 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA E 256 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE E 173 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL E 258 " --> pdb=" O ILE E 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 216 hydrogen bonds defined for protein. 510 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: 6.07 Time building geometry restraints manager: 14.28 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: 9246 1.03 - 1.23: 29 1.23 - 1.42: 4200 1.42 - 1.62: 5523 1.62 - 1.81: 100 Bond restraints: 19098 Sorted by residual: bond pdb=" CA ILE F 733 " pdb=" CB ILE F 733 " ideal model delta sigma weight residual 1.537 1.583 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" CA ILE D 733 " pdb=" CB ILE D 733 " ideal model delta sigma weight residual 1.537 1.583 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" O12 IHP C 501 " pdb=" P2 IHP C 501 " 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 1.611 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O15 IHP C 501 " pdb=" P5 IHP C 501 " ideal model delta sigma weight residual 1.675 1.618 0.057 2.00e-02 2.50e+03 8.25e+00 ... (remaining 19093 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 340 106.33 - 113.24: 21682 113.24 - 120.16: 6379 120.16 - 127.07: 5889 127.07 - 133.99: 114 Bond angle restraints: 34404 Sorted by residual: angle pdb=" C ASN E 369 " pdb=" N LEU E 370 " pdb=" CA LEU E 370 " ideal model delta sigma weight residual 120.28 127.58 -7.30 1.44e+00 4.82e-01 2.57e+01 angle pdb=" C ASN C 369 " pdb=" N LEU C 370 " pdb=" CA LEU C 370 " ideal model delta sigma weight residual 120.28 127.57 -7.29 1.44e+00 4.82e-01 2.56e+01 angle pdb=" C TYR C 358 " pdb=" N LEU C 359 " pdb=" CA LEU C 359 " ideal model delta sigma weight residual 120.44 126.55 -6.11 1.36e+00 5.41e-01 2.02e+01 angle pdb=" C TYR E 358 " pdb=" N LEU E 359 " pdb=" CA LEU E 359 " ideal model delta sigma weight residual 120.44 126.49 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ILE E 362 " pdb=" N LYS E 363 " pdb=" CA LYS E 363 " ideal model delta sigma weight residual 120.44 125.57 -5.13 1.30e+00 5.92e-01 1.56e+01 ... (remaining 34399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 8482 24.12 - 48.25: 469 48.25 - 72.37: 115 72.37 - 96.49: 15 96.49 - 120.61: 12 Dihedral angle restraints: 9093 sinusoidal: 4873 harmonic: 4220 Sorted by residual: 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 180.00 145.50 34.50 0 5.00e+00 4.00e-02 4.76e+01 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 180.00 145.54 34.46 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA ASN C 326 " pdb=" C ASN C 326 " pdb=" N GLU C 327 " pdb=" CA GLU C 327 " ideal model delta harmonic sigma weight residual -180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 9090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 1410 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.026: 0 4.026 - 5.033: 4 Chirality restraints: 1414 Sorted by residual: chirality pdb=" C2 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " 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 E 501 " pdb=" C1 IHP E 501 " pdb=" C3 IHP E 501 " pdb=" O12 IHP E 501 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C3 IHP E 501 " pdb=" C2 IHP E 501 " pdb=" C4 IHP E 501 " pdb=" O13 IHP E 501 " both_signs ideal model delta sigma weight residual False -2.34 2.39 -4.72 2.00e-01 2.50e+01 5.58e+02 ... (remaining 1411 not shown) Planarity restraints: 2840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 754 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO F 755 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 755 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 755 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 754 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 755 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 745 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 746 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 746 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 746 " 0.022 5.00e-02 4.00e+02 ... (remaining 2837 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 3625 2.30 - 3.01: 49477 3.01 - 3.72: 63169 3.72 - 4.43: 94576 4.43 - 5.14: 148534 Nonbonded interactions: 359381 Sorted by model distance: nonbonded pdb=" O LYS B 88 " pdb=" HZ1 LYS B 91 " model vdw 1.589 1.850 nonbonded pdb=" O PHE C 287 " pdb=" HG SER C 290 " model vdw 1.599 1.850 nonbonded pdb=" O PHE E 287 " pdb=" HG SER E 290 " model vdw 1.600 1.850 nonbonded pdb=" O TRP C 312 " pdb=" HG1 THR C 316 " model vdw 1.603 1.850 nonbonded pdb=" OE2 GLU D 837 " pdb=" HG1 THR D 861 " model vdw 1.613 1.850 ... (remaining 359376 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)) } 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 501 through 504)) selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 4.880 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: 0.310 Extract box with map and model: 13.760 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 67.980 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 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 : 0.005 0.065 9825 Z= 0.343 Angle : 0.832 8.412 13301 Z= 0.446 Chirality : 0.266 5.033 1414 Planarity : 0.004 0.051 1708 Dihedral : 16.347 120.615 3693 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.39 % Allowed : 2.76 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % 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: -3.35 (0.23), residues: 1172 helix: -2.40 (0.19), residues: 405 sheet: -3.25 (0.43), residues: 100 loop : -1.92 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 753 HIS 0.005 0.001 HIS C 33 PHE 0.009 0.002 PHE C 205 TYR 0.017 0.002 TYR C 24 ARG 0.006 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 1.788 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: C 87 TYR cc_start: 0.4943 (m-80) cc_final: 0.4590 (m-80) REVERT: C 160 ILE cc_start: 0.7763 (mt) cc_final: 0.7505 (mt) REVERT: C 174 ASP cc_start: 0.7053 (t0) cc_final: 0.6842 (t0) REVERT: E 260 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7955 (tm-30) REVERT: E 297 MET cc_start: 0.6940 (mtp) cc_final: 0.6685 (ttm) REVERT: A 65 ILE cc_start: 0.6307 (pt) cc_final: 0.5982 (pt) REVERT: B 88 LYS cc_start: 0.8931 (mttt) cc_final: 0.8274 (tptt) REVERT: F 745 ASP cc_start: 0.4122 (t0) cc_final: 0.3347 (t0) REVERT: F 808 LYS cc_start: 0.6166 (mttt) cc_final: 0.5308 (ptpt) outliers start: 4 outliers final: 0 residues processed: 305 average time/residue: 0.5509 time to fit residues: 227.4834 Evaluate side-chains 211 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 HIS ** C 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 292 ASN E 57 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 353 GLN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 724 ASN D 724 ASN D 730 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9825 Z= 0.223 Angle : 0.654 10.047 13301 Z= 0.331 Chirality : 0.040 0.381 1414 Planarity : 0.005 0.051 1708 Dihedral : 6.593 53.713 1391 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.99 % Allowed : 10.55 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1172 helix: -1.04 (0.22), residues: 439 sheet: -3.33 (0.43), residues: 100 loop : -1.88 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 753 HIS 0.004 0.001 HIS E 167 PHE 0.009 0.001 PHE C 241 TYR 0.015 0.001 TYR C 24 ARG 0.008 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 221 time to evaluate : 1.602 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: C 87 TYR cc_start: 0.4891 (m-80) cc_final: 0.4530 (m-80) REVERT: C 140 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6673 (p90) REVERT: C 174 ASP cc_start: 0.7529 (t0) cc_final: 0.7212 (t0) REVERT: C 289 LYS cc_start: 0.8273 (tttm) cc_final: 0.7905 (tptm) REVERT: E 289 LYS cc_start: 0.8025 (tttm) cc_final: 0.7780 (tptm) REVERT: B 88 LYS cc_start: 0.9081 (mttt) cc_final: 0.8703 (tptt) REVERT: B 113 LEU cc_start: 0.8972 (mp) cc_final: 0.8721 (mp) REVERT: F 808 LYS cc_start: 0.5739 (mttt) cc_final: 0.5193 (ptpt) REVERT: F 849 LYS cc_start: 0.6512 (tptt) cc_final: 0.5501 (ttmt) outliers start: 10 outliers final: 5 residues processed: 225 average time/residue: 0.4605 time to fit residues: 144.2835 Evaluate side-chains 208 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 826 HIS D 747 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9825 Z= 0.200 Angle : 0.594 9.178 13301 Z= 0.303 Chirality : 0.038 0.176 1414 Planarity : 0.004 0.043 1708 Dihedral : 6.216 45.323 1391 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.99 % Allowed : 12.52 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.24), residues: 1172 helix: -0.83 (0.22), residues: 432 sheet: -3.17 (0.46), residues: 100 loop : -1.84 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 753 HIS 0.006 0.001 HIS C 140 PHE 0.008 0.001 PHE D 781 TYR 0.013 0.001 TYR E 166 ARG 0.005 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 1.616 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: C 204 TYR cc_start: 0.5858 (t80) cc_final: 0.5335 (t80) REVERT: A 111 GLU cc_start: 0.7916 (pp20) cc_final: 0.7584 (pp20) REVERT: B 88 LYS cc_start: 0.9028 (mttt) cc_final: 0.8650 (tptt) REVERT: F 808 LYS cc_start: 0.5841 (mttt) cc_final: 0.5446 (ptpt) REVERT: F 849 LYS cc_start: 0.6334 (tptt) cc_final: 0.5443 (ttmt) REVERT: D 870 PHE cc_start: 0.6374 (t80) cc_final: 0.6109 (t80) outliers start: 10 outliers final: 6 residues processed: 219 average time/residue: 0.4496 time to fit residues: 139.7411 Evaluate side-chains 204 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9825 Z= 0.230 Angle : 0.609 9.014 13301 Z= 0.313 Chirality : 0.039 0.165 1414 Planarity : 0.004 0.044 1708 Dihedral : 6.485 57.280 1391 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 1.18 % Allowed : 15.98 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.24), residues: 1172 helix: -0.77 (0.23), residues: 459 sheet: -3.28 (0.48), residues: 100 loop : -2.04 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 753 HIS 0.004 0.001 HIS E 33 PHE 0.011 0.001 PHE F 870 TYR 0.013 0.001 TYR E 24 ARG 0.006 0.001 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 204 time to evaluate : 1.592 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: A 111 GLU cc_start: 0.7974 (pp20) cc_final: 0.7733 (pp20) REVERT: B 90 MET cc_start: 0.8054 (tpp) cc_final: 0.7629 (tpp) REVERT: F 808 LYS cc_start: 0.6051 (mttt) cc_final: 0.5690 (ptpt) REVERT: F 849 LYS cc_start: 0.6378 (tptt) cc_final: 0.5507 (ttmt) REVERT: F 870 PHE cc_start: 0.6665 (t80) cc_final: 0.5817 (t80) REVERT: D 754 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7473 (mm-40) REVERT: D 804 GLU cc_start: 0.7436 (tp30) cc_final: 0.7162 (tp30) outliers start: 12 outliers final: 8 residues processed: 209 average time/residue: 0.4203 time to fit residues: 126.6121 Evaluate side-chains 197 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain D residue 754 GLN Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 HIS ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9825 Z= 0.307 Angle : 0.686 10.498 13301 Z= 0.359 Chirality : 0.040 0.150 1414 Planarity : 0.005 0.048 1708 Dihedral : 7.037 59.964 1391 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.56 % Allowed : 17.75 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.23), residues: 1172 helix: -0.90 (0.22), residues: 458 sheet: -3.45 (0.48), residues: 100 loop : -2.27 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 753 HIS 0.005 0.001 HIS C 33 PHE 0.017 0.002 PHE B 92 TYR 0.017 0.002 TYR E 24 ARG 0.005 0.001 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.490 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: C 48 TYR cc_start: 0.8691 (p90) cc_final: 0.8396 (p90) REVERT: C 140 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6643 (p-80) REVERT: C 204 TYR cc_start: 0.6178 (t80) cc_final: 0.5717 (t80) REVERT: C 205 PHE cc_start: 0.8367 (t80) cc_final: 0.8153 (t80) REVERT: B 84 THR cc_start: 0.8170 (p) cc_final: 0.7946 (p) REVERT: F 808 LYS cc_start: 0.6075 (mttt) cc_final: 0.5732 (ptpt) REVERT: F 849 LYS cc_start: 0.6357 (tptt) cc_final: 0.5570 (ttmt) REVERT: D 804 GLU cc_start: 0.7496 (tp30) cc_final: 0.7225 (tp30) REVERT: D 849 LYS cc_start: 0.6009 (tptt) cc_final: 0.5320 (ttmt) outliers start: 26 outliers final: 14 residues processed: 221 average time/residue: 0.4622 time to fit residues: 146.7007 Evaluate side-chains 207 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 192 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 845 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 GLN C 140 HIS ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9825 Z= 0.262 Angle : 0.640 9.747 13301 Z= 0.331 Chirality : 0.039 0.135 1414 Planarity : 0.005 0.047 1708 Dihedral : 7.001 58.523 1391 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 1.58 % Allowed : 19.63 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.23), residues: 1172 helix: -0.77 (0.23), residues: 460 sheet: -3.38 (0.50), residues: 100 loop : -2.33 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 753 HIS 0.018 0.001 HIS C 140 PHE 0.011 0.001 PHE F 852 TYR 0.011 0.001 TYR C 330 ARG 0.006 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.618 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: C 48 TYR cc_start: 0.8614 (p90) cc_final: 0.8143 (p90) REVERT: C 297 MET cc_start: 0.7356 (mtm) cc_final: 0.7079 (mtp) REVERT: F 808 LYS cc_start: 0.6039 (mttt) cc_final: 0.5718 (ptpt) REVERT: F 849 LYS cc_start: 0.6400 (tptt) cc_final: 0.5639 (ttmt) REVERT: D 804 GLU cc_start: 0.7529 (tp30) cc_final: 0.7287 (tp30) REVERT: D 849 LYS cc_start: 0.6080 (tptt) cc_final: 0.5469 (ttmt) outliers start: 16 outliers final: 12 residues processed: 209 average time/residue: 0.4519 time to fit residues: 136.0346 Evaluate side-chains 202 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 845 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9825 Z= 0.202 Angle : 0.592 8.790 13301 Z= 0.305 Chirality : 0.038 0.140 1414 Planarity : 0.004 0.044 1708 Dihedral : 6.832 57.356 1391 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 1.68 % Allowed : 20.32 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.23), residues: 1172 helix: -0.60 (0.23), residues: 460 sheet: -3.23 (0.51), residues: 100 loop : -2.36 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 753 HIS 0.004 0.001 HIS E 199 PHE 0.011 0.001 PHE C 205 TYR 0.018 0.001 TYR C 172 ARG 0.002 0.000 ARG D 838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 TYR cc_start: 0.8390 (p90) cc_final: 0.8133 (p90) REVERT: C 297 MET cc_start: 0.7289 (mtm) cc_final: 0.7071 (mtp) REVERT: E 79 ILE cc_start: 0.7925 (tp) cc_final: 0.7597 (tt) REVERT: A 111 GLU cc_start: 0.7952 (pp20) cc_final: 0.7639 (pp20) REVERT: F 808 LYS cc_start: 0.5926 (mttt) cc_final: 0.5714 (ptpt) REVERT: F 828 THR cc_start: 0.3000 (OUTLIER) cc_final: 0.2750 (p) REVERT: D 804 GLU cc_start: 0.7585 (tp30) cc_final: 0.7336 (tp30) outliers start: 17 outliers final: 14 residues processed: 205 average time/residue: 0.4426 time to fit residues: 129.2939 Evaluate side-chains 205 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 773 LEU Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain F residue 828 THR Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0050 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9825 Z= 0.246 Angle : 0.630 9.421 13301 Z= 0.326 Chirality : 0.039 0.133 1414 Planarity : 0.005 0.047 1708 Dihedral : 6.977 58.509 1391 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 2.47 % Allowed : 20.02 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.23), residues: 1172 helix: -0.58 (0.23), residues: 473 sheet: -3.38 (0.50), residues: 100 loop : -2.56 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 753 HIS 0.004 0.001 HIS D 826 PHE 0.013 0.002 PHE C 205 TYR 0.017 0.002 TYR C 172 ARG 0.007 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.479 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: C 48 TYR cc_start: 0.8407 (p90) cc_final: 0.8145 (p90) REVERT: C 166 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.4924 (m-80) REVERT: E 36 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8427 (ttm-80) REVERT: E 79 ILE cc_start: 0.7963 (tp) cc_final: 0.7570 (tt) REVERT: A 111 GLU cc_start: 0.7975 (pp20) cc_final: 0.7734 (pp20) REVERT: B 77 SER cc_start: 0.8203 (m) cc_final: 0.7670 (t) REVERT: D 804 GLU cc_start: 0.7729 (tp30) cc_final: 0.7516 (tp30) REVERT: D 828 THR cc_start: 0.3406 (OUTLIER) cc_final: 0.3159 (p) outliers start: 25 outliers final: 20 residues processed: 212 average time/residue: 0.4363 time to fit residues: 133.7439 Evaluate side-chains 216 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 724 ASN Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 828 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 105 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9825 Z= 0.208 Angle : 0.604 8.739 13301 Z= 0.308 Chirality : 0.038 0.135 1414 Planarity : 0.004 0.044 1708 Dihedral : 6.825 57.680 1391 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.17 % Allowed : 21.01 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1172 helix: -0.46 (0.23), residues: 475 sheet: -3.32 (0.50), residues: 100 loop : -2.48 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 312 HIS 0.004 0.001 HIS C 33 PHE 0.010 0.001 PHE C 205 TYR 0.020 0.001 TYR D 827 ARG 0.005 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 1.475 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: C 166 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.4868 (m-80) REVERT: E 36 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8410 (ttm-80) REVERT: E 79 ILE cc_start: 0.7961 (tp) cc_final: 0.7564 (tt) REVERT: A 111 GLU cc_start: 0.7960 (pp20) cc_final: 0.7755 (pp20) REVERT: B 77 SER cc_start: 0.8178 (m) cc_final: 0.7678 (t) REVERT: B 90 MET cc_start: 0.8092 (tpp) cc_final: 0.7637 (tpp) REVERT: B 123 GLU cc_start: 0.7943 (tp30) cc_final: 0.7673 (tp30) outliers start: 22 outliers final: 16 residues processed: 211 average time/residue: 0.4156 time to fit residues: 125.8710 Evaluate side-chains 213 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 196 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 113 optimal weight: 0.0770 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9825 Z= 0.183 Angle : 0.596 8.836 13301 Z= 0.302 Chirality : 0.037 0.148 1414 Planarity : 0.004 0.045 1708 Dihedral : 6.620 57.683 1391 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.58 % Allowed : 21.60 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.23), residues: 1172 helix: -0.30 (0.23), residues: 468 sheet: -3.20 (0.51), residues: 100 loop : -2.38 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 312 HIS 0.003 0.001 HIS C 33 PHE 0.009 0.001 PHE B 86 TYR 0.018 0.001 TYR C 172 ARG 0.006 0.000 ARG C 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 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 MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 2.471 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: C 79 ILE cc_start: 0.7814 (tp) cc_final: 0.7448 (tt) REVERT: C 166 TYR cc_start: 0.5908 (OUTLIER) cc_final: 0.4731 (m-80) REVERT: E 36 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8405 (ttm-80) REVERT: E 79 ILE cc_start: 0.7949 (tp) cc_final: 0.7542 (tt) REVERT: B 77 SER cc_start: 0.8204 (m) cc_final: 0.7691 (t) REVERT: B 90 MET cc_start: 0.8062 (tpp) cc_final: 0.7578 (tpp) REVERT: D 729 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.4179 (p90) outliers start: 16 outliers final: 13 residues processed: 206 average time/residue: 0.4185 time to fit residues: 124.3664 Evaluate side-chains 210 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 747 HIS ** 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 = 0.4290 r_free = 0.4290 target = 0.162372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.141405 restraints weight = 81020.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.147278 restraints weight = 35777.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.151198 restraints weight = 19806.320| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4151 r_free = 0.4151 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4151 r_free = 0.4151 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9825 Z= 0.199 Angle : 0.597 8.145 13301 Z= 0.305 Chirality : 0.038 0.119 1414 Planarity : 0.004 0.044 1708 Dihedral : 6.530 56.412 1391 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 1.87 % Allowed : 21.20 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 1172 helix: -0.26 (0.23), residues: 464 sheet: -3.04 (0.53), residues: 94 loop : -2.42 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 753 HIS 0.004 0.001 HIS C 33 PHE 0.010 0.001 PHE C 205 TYR 0.024 0.001 TYR D 827 ARG 0.005 0.000 ARG C 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.43 seconds wall clock time: 84 minutes 58.85 seconds (5098.85 seconds total)