Starting phenix.real_space_refine on Wed Feb 21 17:40:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aml_11822/02_2024/7aml_11822_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aml_11822/02_2024/7aml_11822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aml_11822/02_2024/7aml_11822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aml_11822/02_2024/7aml_11822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aml_11822/02_2024/7aml_11822_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7aml_11822/02_2024/7aml_11822_trim.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 S 134 5.16 5 C 9986 2.51 5 N 2762 2.21 5 O 3128 1.98 5 H 15286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 353": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 467": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 549": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 614": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 28": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 242": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 272": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 286": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 351": "OE1" <-> "OE2" Residue "D ARG 353": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 467": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D ARG 505": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 542": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 549": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 579": "OD1" <-> "OD2" Residue "D ARG 591": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 614": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 337": "OD1" <-> "OD2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 130": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 287": "OD1" <-> "OD2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 337": "OD1" <-> "OD2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F GLU 177": "OE1" <-> "OE2" Residue "F ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31304 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9267 Classifications: {'peptide': 596} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 565} Chain: "D" Number of atoms: 9267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9267 Classifications: {'peptide': 596} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 565} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4719 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain breaks: 2 Chain: "C" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1550 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "E" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4719 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain breaks: 2 Chain: "F" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1550 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.79, per 1000 atoms: 0.47 Number of scatterers: 31304 At special positions: 0 Unit cell: (180.36, 167.4, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 134 16.00 O 3128 8.00 N 2762 7.00 C 9986 6.00 H 15286 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 123 " distance=2.02 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 536 " distance=2.02 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 580 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 612 " distance=2.04 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 123 " distance=2.02 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 183 " distance=2.05 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 415 " distance=2.03 Simple disulfide: pdb=" SG CYS D 441 " - pdb=" SG CYS D 471 " distance=2.02 Simple disulfide: pdb=" SG CYS D 514 " - pdb=" SG CYS D 536 " distance=2.02 Simple disulfide: pdb=" SG CYS D 523 " - pdb=" SG CYS D 553 " distance=2.03 Simple disulfide: pdb=" SG CYS D 560 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 565 " - pdb=" SG CYS D 580 " distance=2.03 Simple disulfide: pdb=" SG CYS D 603 " - pdb=" SG CYS D 612 " distance=2.04 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS D 610 " distance=2.03 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 214 " distance=2.02 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 192 " distance=2.02 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 203 " distance=2.02 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 232 " distance=2.02 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 202 " - pdb=" SG CYS F 202 " distance=2.04 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 45 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 102 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 214 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 192 " distance=2.02 Simple disulfide: pdb=" SG CYS E 187 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 216 " - pdb=" SG CYS E 224 " distance=2.02 Simple disulfide: pdb=" SG CYS E 246 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 270 " - pdb=" SG CYS E 288 " distance=2.02 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 328 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 203 " distance=2.05 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 232 " distance=2.03 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 705 " - " ASN A 259 " " NAG A 706 " - " ASN A 308 " " NAG A 707 " - " ASN A 346 " " NAG A 708 " - " ASN A 362 " " NAG A 709 " - " ASN A 378 " " NAG A 710 " - " ASN A 461 " " NAG A 711 " - " ASN A 572 " " NAG C 301 " - " ASN C 150 " " NAG D 705 " - " ASN D 259 " " NAG D 706 " - " ASN D 308 " " NAG D 707 " - " ASN D 346 " " NAG D 708 " - " ASN D 362 " " NAG D 709 " - " ASN D 378 " " NAG D 710 " - " ASN D 461 " " NAG D 711 " - " ASN D 572 " " NAG F 301 " - " ASN F 150 " Time building additional restraints: 23.93 Conformation dependent library (CDL) restraints added in 3.6 seconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3776 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 34 sheets defined 28.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.685A pdb=" N PHE A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 94 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 96' Processing helix chain 'A' and resid 119 through 123 removed outlier: 4.082A pdb=" N CYS A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.776A pdb=" N ILE A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.781A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.176A pdb=" N CYS A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 89 through 96 removed outlier: 3.684A pdb=" N PHE D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 94 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 96' Processing helix chain 'D' and resid 119 through 123 removed outlier: 4.082A pdb=" N CYS D 123 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.901A pdb=" N SER D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 182 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS D 183 " --> pdb=" O HIS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 468 through 471 removed outlier: 3.577A pdb=" N CYS D 471 " --> pdb=" O ARG D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 468 through 471' Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.781A pdb=" N ALA D 525 " --> pdb=" O GLY D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.184A pdb=" N CYS D 580 " --> pdb=" O CYS D 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.853A pdb=" N ASP B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.806A pdb=" N HIS B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 removed outlier: 4.172A pdb=" N SER B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.592A pdb=" N SER B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.738A pdb=" N LYS B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 4.395A pdb=" N GLY B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.533A pdb=" N GLU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.942A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 removed outlier: 4.220A pdb=" N CYS B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 337 removed outlier: 3.727A pdb=" N CYS B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.690A pdb=" N ARG B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.853A pdb=" N ASP E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.807A pdb=" N HIS E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 136 removed outlier: 4.171A pdb=" N SER E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 removed outlier: 3.592A pdb=" N SER E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 165 through 173 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 188 through 203 removed outlier: 3.739A pdb=" N LYS E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 removed outlier: 4.395A pdb=" N GLY E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET E 211 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.530A pdb=" N GLU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 245 through 254 Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.941A pdb=" N PHE E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 4.220A pdb=" N CYS E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 289 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.726A pdb=" N CYS E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 350 removed outlier: 3.690A pdb=" N ARG E 342 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 349 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 178 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 34 removed outlier: 3.958A pdb=" N TYR A 30 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 132 " --> pdb=" O TYR A 30 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 32 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 134 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 34 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 129 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 111 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 133 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 110 " --> pdb=" O CYS A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.928A pdb=" N LEU A 45 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.848A pdb=" N ILE A 162 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 238 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 240 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 244 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 223 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 191 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 6.863A pdb=" N LEU A 209 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 210 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 removed outlier: 6.935A pdb=" N GLU A 264 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR A 380 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 355 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 281 through 285 removed outlier: 3.517A pdb=" N LYS A 340 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.776A pdb=" N VAL A 302 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 361 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 373 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.751A pdb=" N THR A 455 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 450 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 429 removed outlier: 3.718A pdb=" N THR A 491 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AB3, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AB4, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 34 removed outlier: 3.959A pdb=" N TYR D 30 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 132 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 32 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 134 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 34 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 129 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 111 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 133 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS D 110 " --> pdb=" O CYS D 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.876A pdb=" N LEU D 45 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 163 removed outlier: 6.848A pdb=" N ILE D 162 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 238 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 240 " --> pdb=" O CYS D 229 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 244 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 223 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 191 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 170 through 173 removed outlier: 6.864A pdb=" N LEU D 209 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 210 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 264 through 265 removed outlier: 6.935A pdb=" N GLU D 264 " --> pdb=" O ASN D 378 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR D 380 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 355 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 281 through 285 removed outlier: 3.516A pdb=" N LYS D 340 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 281 through 285 Processing sheet with id=AC3, first strand: chain 'D' and resid 302 through 305 removed outlier: 3.775A pdb=" N VAL D 302 " --> pdb=" O ASN D 362 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 361 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 373 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.620A pdb=" N THR D 455 " --> pdb=" O ASN D 450 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN D 450 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 423 through 429 removed outlier: 3.718A pdb=" N THR D 491 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'D' and resid 585 through 587 Processing sheet with id=AC8, first strand: chain 'D' and resid 589 through 591 Processing sheet with id=AC9, first strand: chain 'B' and resid 303 through 304 removed outlier: 4.021A pdb=" N ASN B 303 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 313 " --> pdb=" O ASN B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 143 through 150 Processing sheet with id=AD2, first strand: chain 'C' and resid 202 through 208 removed outlier: 3.806A pdb=" N ALA C 233 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 206 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS C 231 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE C 208 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA C 229 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 212 through 215 Processing sheet with id=AD4, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.022A pdb=" N ASN E 303 " --> pdb=" O SER E 313 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER E 313 " --> pdb=" O ASN E 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 144 through 150 Processing sheet with id=AD6, first strand: chain 'F' and resid 202 through 205 removed outlier: 3.512A pdb=" N CYS F 202 " --> pdb=" O VAL F 235 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 212 through 215 431 hydrogen bonds defined for protein. 1155 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: 10.46 Time building geometry restraints manager: 24.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15286 1.02 - 1.23: 24 1.23 - 1.43: 6850 1.43 - 1.63: 9302 1.63 - 1.84: 154 Bond restraints: 31616 Sorted by residual: bond pdb=" ND2 ASN A 452 " pdb="HD21 ASN A 452 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 452 " pdb="HD22 ASN A 452 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 185 " pdb="HD21 ASN A 185 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 295 " pdb="HD21 ASN A 295 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 295 " pdb="HD22 ASN A 295 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 31611 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.47: 376 105.47 - 112.59: 35929 112.59 - 119.71: 8289 119.71 - 126.82: 12154 126.82 - 133.94: 190 Bond angle restraints: 56938 Sorted by residual: angle pdb=" N SER B 222 " pdb=" CA SER B 222 " pdb=" C SER B 222 " ideal model delta sigma weight residual 109.07 98.35 10.72 1.61e+00 3.86e-01 4.43e+01 angle pdb=" N SER E 222 " pdb=" CA SER E 222 " pdb=" C SER E 222 " ideal model delta sigma weight residual 109.07 98.92 10.15 1.61e+00 3.86e-01 3.97e+01 angle pdb=" N ASP D 562 " pdb=" CA ASP D 562 " pdb=" C ASP D 562 " ideal model delta sigma weight residual 111.02 118.01 -6.99 1.22e+00 6.72e-01 3.28e+01 angle pdb=" N SER A 142 " pdb=" CA SER A 142 " pdb=" C SER A 142 " ideal model delta sigma weight residual 109.76 101.15 8.61 1.59e+00 3.96e-01 2.93e+01 angle pdb=" N SER D 142 " pdb=" CA SER D 142 " pdb=" C SER D 142 " ideal model delta sigma weight residual 110.28 102.58 7.70 1.48e+00 4.57e-01 2.71e+01 ... (remaining 56933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 13704 16.43 - 32.85: 1191 32.85 - 49.28: 347 49.28 - 65.70: 117 65.70 - 82.13: 16 Dihedral angle restraints: 15375 sinusoidal: 8581 harmonic: 6794 Sorted by residual: dihedral pdb=" CB CYS B 187 " pdb=" SG CYS B 187 " pdb=" SG CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sinusoidal sigma weight residual -86.00 -139.18 53.18 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS E 187 " pdb=" SG CYS E 187 " pdb=" SG CYS E 236 " pdb=" CB CYS E 236 " ideal model delta sinusoidal sigma weight residual -86.00 -139.15 53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS C 169 " pdb=" SG CYS C 169 " pdb=" SG CYS C 232 " pdb=" CB CYS C 232 " ideal model delta sinusoidal sigma weight residual 93.00 145.04 -52.04 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 15372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2465 0.187 - 0.374: 19 0.374 - 0.560: 0 0.560 - 0.747: 0 0.747 - 0.934: 2 Chirality restraints: 2486 Sorted by residual: chirality pdb=" C1 NAG A 707 " pdb=" ND2 ASN A 346 " pdb=" C2 NAG A 707 " pdb=" O5 NAG A 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG D 707 " pdb=" ND2 ASN D 346 " pdb=" C2 NAG D 707 " pdb=" O5 NAG D 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG D 711 " pdb=" ND2 ASN D 572 " pdb=" C2 NAG D 711 " pdb=" O5 NAG D 711 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2483 not shown) Planarity restraints: 4774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 185 " 0.001 2.00e-02 2.50e+03 1.94e-01 4.68e+02 pdb=" CG ASN A 185 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 185 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN A 185 " 0.319 2.00e-02 2.50e+03 pdb="HD21 ASN A 185 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 203 " 0.042 2.00e-02 2.50e+03 7.73e-02 5.97e+01 pdb=" N ARG F 204 " -0.133 2.00e-02 2.50e+03 pdb=" CA ARG F 204 " 0.035 2.00e-02 2.50e+03 pdb=" H ARG F 204 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 206 " -0.033 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" N ALA F 207 " 0.112 2.00e-02 2.50e+03 pdb=" CA ALA F 207 " -0.032 2.00e-02 2.50e+03 pdb=" H ALA F 207 " -0.046 2.00e-02 2.50e+03 ... (remaining 4771 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1009 2.13 - 2.75: 56840 2.75 - 3.37: 78737 3.37 - 3.98: 98238 3.98 - 4.60: 153003 Nonbonded interactions: 387827 Sorted by model distance: nonbonded pdb=" OE1 GLU A 482 " pdb=" H ASN A 485 " model vdw 1.516 1.850 nonbonded pdb=" OE1 GLU D 482 " pdb=" H ASN D 485 " model vdw 1.517 1.850 nonbonded pdb=" OE1 GLN A 416 " pdb=" H GLN A 416 " model vdw 1.539 1.850 nonbonded pdb=" OE1 GLN D 416 " pdb=" H GLN D 416 " model vdw 1.539 1.850 nonbonded pdb=" H GLU D 274 " pdb=" OD1 ASN D 346 " model vdw 1.554 1.850 ... (remaining 387822 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' 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=0.88 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: 4.410 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: 0.480 Extract box with map and model: 8.510 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 95.730 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16330 Z= 0.369 Angle : 0.836 10.720 22104 Z= 0.481 Chirality : 0.058 0.934 2486 Planarity : 0.004 0.050 2872 Dihedral : 13.362 82.127 6396 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.84 % Allowed : 1.51 % Favored : 97.66 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.16), residues: 1976 helix: -2.22 (0.23), residues: 396 sheet: -2.19 (0.24), residues: 370 loop : -2.66 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 107 HIS 0.004 0.001 HIS A 74 PHE 0.036 0.002 PHE F 166 TYR 0.043 0.002 TYR E 110 ARG 0.014 0.001 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 2.834 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: A 183 CYS cc_start: 0.1496 (OUTLIER) cc_final: 0.0982 (t) REVERT: A 565 CYS cc_start: 0.3962 (OUTLIER) cc_final: 0.3664 (p) outliers start: 15 outliers final: 9 residues processed: 198 average time/residue: 0.6063 time to fit residues: 178.3573 Evaluate side-chains 144 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 580 CYS Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain F residue 169 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 HIS ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16330 Z= 0.238 Angle : 0.612 7.339 22104 Z= 0.319 Chirality : 0.049 0.615 2486 Planarity : 0.005 0.039 2872 Dihedral : 7.654 71.618 2551 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.45 % Allowed : 5.69 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.17), residues: 1976 helix: -1.49 (0.24), residues: 414 sheet: -1.62 (0.23), residues: 428 loop : -2.52 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 538 HIS 0.005 0.001 HIS B 207 PHE 0.024 0.002 PHE D 611 TYR 0.012 0.002 TYR B 110 ARG 0.005 0.000 ARG D 591 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 2.348 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: E 315 PHE cc_start: 0.5803 (t80) cc_final: 0.5339 (t80) outliers start: 26 outliers final: 20 residues processed: 163 average time/residue: 0.6055 time to fit residues: 145.5457 Evaluate side-chains 145 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 564 TYR Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 187 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 187 CYS Chi-restraints excluded: chain F residue 169 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16330 Z= 0.200 Angle : 0.539 6.525 22104 Z= 0.280 Chirality : 0.045 0.570 2486 Planarity : 0.004 0.046 2872 Dihedral : 6.824 57.688 2545 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.67 % Allowed : 7.64 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.82 (0.17), residues: 1976 helix: -1.07 (0.25), residues: 418 sheet: -1.54 (0.24), residues: 406 loop : -2.39 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 538 HIS 0.004 0.001 HIS C 227 PHE 0.022 0.001 PHE F 214 TYR 0.020 0.001 TYR B 110 ARG 0.004 0.000 ARG D 591 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 315 PHE cc_start: 0.6136 (t80) cc_final: 0.5591 (t80) outliers start: 30 outliers final: 20 residues processed: 164 average time/residue: 0.6313 time to fit residues: 153.1366 Evaluate side-chains 142 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 564 TYR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 0.2980 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16330 Z= 0.157 Angle : 0.504 6.413 22104 Z= 0.258 Chirality : 0.044 0.512 2486 Planarity : 0.003 0.040 2872 Dihedral : 6.311 56.639 2539 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.17 % Allowed : 10.42 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.18), residues: 1976 helix: -0.72 (0.25), residues: 418 sheet: -1.47 (0.24), residues: 434 loop : -2.23 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 538 HIS 0.003 0.001 HIS D 337 PHE 0.017 0.001 PHE C 214 TYR 0.018 0.001 TYR B 106 ARG 0.002 0.000 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 2.636 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: E 93 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6992 (mttp) outliers start: 21 outliers final: 17 residues processed: 155 average time/residue: 0.5984 time to fit residues: 139.2770 Evaluate side-chains 141 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 TYR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 2 optimal weight: 0.0170 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 HIS ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16330 Z= 0.260 Angle : 0.584 7.673 22104 Z= 0.304 Chirality : 0.046 0.533 2486 Planarity : 0.004 0.045 2872 Dihedral : 6.543 58.291 2539 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.73 % Allowed : 11.04 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.80 (0.17), residues: 1976 helix: -1.17 (0.24), residues: 432 sheet: -1.39 (0.23), residues: 466 loop : -2.42 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 107 HIS 0.006 0.001 HIS D 337 PHE 0.029 0.002 PHE C 214 TYR 0.014 0.002 TYR C 168 ARG 0.005 0.000 ARG D 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 2.640 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: D 607 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6188 (mm-30) outliers start: 31 outliers final: 27 residues processed: 152 average time/residue: 0.6062 time to fit residues: 140.9489 Evaluate side-chains 152 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16330 Z= 0.235 Angle : 0.552 7.099 22104 Z= 0.286 Chirality : 0.045 0.503 2486 Planarity : 0.004 0.054 2872 Dihedral : 6.267 55.964 2537 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.67 % Allowed : 11.87 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.76 (0.17), residues: 1976 helix: -1.17 (0.24), residues: 432 sheet: -1.34 (0.23), residues: 478 loop : -2.39 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 107 HIS 0.005 0.001 HIS C 222 PHE 0.025 0.001 PHE F 214 TYR 0.015 0.002 TYR E 106 ARG 0.004 0.000 ARG D 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 2.657 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 outliers start: 30 outliers final: 28 residues processed: 151 average time/residue: 0.6044 time to fit residues: 135.3654 Evaluate side-chains 148 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 TYR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.0010 chunk 159 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 188 optimal weight: 0.3980 chunk 118 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16330 Z= 0.180 Angle : 0.516 6.827 22104 Z= 0.264 Chirality : 0.043 0.481 2486 Planarity : 0.004 0.041 2872 Dihedral : 5.986 58.633 2537 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.73 % Allowed : 12.49 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.59 (0.18), residues: 1976 helix: -0.87 (0.24), residues: 432 sheet: -1.31 (0.24), residues: 454 loop : -2.31 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 538 HIS 0.003 0.001 HIS C 222 PHE 0.017 0.001 PHE F 214 TYR 0.028 0.001 TYR E 106 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 2.808 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: E 333 GLU cc_start: 0.4896 (OUTLIER) cc_final: 0.3811 (tm-30) outliers start: 31 outliers final: 27 residues processed: 157 average time/residue: 0.6177 time to fit residues: 142.9440 Evaluate side-chains 149 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16330 Z= 0.161 Angle : 0.506 6.842 22104 Z= 0.259 Chirality : 0.043 0.461 2486 Planarity : 0.004 0.042 2872 Dihedral : 5.818 59.396 2537 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.56 % Allowed : 13.21 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.45 (0.18), residues: 1976 helix: -0.72 (0.24), residues: 444 sheet: -1.21 (0.24), residues: 454 loop : -2.26 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 538 HIS 0.004 0.001 HIS D 600 PHE 0.015 0.001 PHE F 214 TYR 0.024 0.001 TYR B 106 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 2.885 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: A 230 MET cc_start: 0.4573 (mpp) cc_final: 0.3970 (mtm) REVERT: E 333 GLU cc_start: 0.4822 (OUTLIER) cc_final: 0.3552 (tm-30) outliers start: 28 outliers final: 24 residues processed: 147 average time/residue: 0.6447 time to fit residues: 140.9036 Evaluate side-chains 143 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 TYR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 0.0980 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 159 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16330 Z= 0.144 Angle : 0.497 11.648 22104 Z= 0.252 Chirality : 0.042 0.435 2486 Planarity : 0.003 0.042 2872 Dihedral : 5.564 59.785 2537 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.23 % Allowed : 13.66 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.14 (0.18), residues: 1976 helix: -0.34 (0.25), residues: 432 sheet: -1.05 (0.24), residues: 450 loop : -2.08 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 538 HIS 0.005 0.001 HIS D 600 PHE 0.008 0.001 PHE F 214 TYR 0.029 0.001 TYR B 106 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 2.749 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: A 230 MET cc_start: 0.4803 (mpp) cc_final: 0.4072 (mtm) outliers start: 22 outliers final: 19 residues processed: 138 average time/residue: 0.6120 time to fit residues: 125.6817 Evaluate side-chains 136 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 TYR Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 ASN ** F 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16330 Z= 0.168 Angle : 0.511 10.713 22104 Z= 0.260 Chirality : 0.043 0.426 2486 Planarity : 0.003 0.042 2872 Dihedral : 5.559 58.316 2537 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.39 % Allowed : 13.43 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.12 (0.18), residues: 1976 helix: -0.35 (0.25), residues: 432 sheet: -1.06 (0.24), residues: 454 loop : -2.05 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 538 HIS 0.003 0.001 HIS A 600 PHE 0.014 0.001 PHE F 214 TYR 0.023 0.001 TYR B 106 ARG 0.007 0.000 ARG B 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 2.725 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: A 230 MET cc_start: 0.4841 (mpp) cc_final: 0.4075 (mtm) REVERT: D 230 MET cc_start: 0.5080 (mpp) cc_final: 0.3969 (mtm) outliers start: 25 outliers final: 22 residues processed: 139 average time/residue: 0.6125 time to fit residues: 127.9344 Evaluate side-chains 138 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 TYR Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 603 CYS Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.218096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.185520 restraints weight = 80597.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.187070 restraints weight = 55473.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.188669 restraints weight = 38530.992| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4394 r_free = 0.4394 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16330 Z= 0.189 Angle : 0.528 9.436 22104 Z= 0.271 Chirality : 0.043 0.411 2486 Planarity : 0.004 0.041 2872 Dihedral : 5.665 54.595 2537 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.45 % Allowed : 13.55 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.21 (0.18), residues: 1976 helix: -0.55 (0.25), residues: 436 sheet: -1.10 (0.24), residues: 458 loop : -2.05 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 107 HIS 0.004 0.001 HIS C 222 PHE 0.020 0.001 PHE C 214 TYR 0.038 0.001 TYR B 106 ARG 0.004 0.000 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5386.25 seconds wall clock time: 96 minutes 54.22 seconds (5814.22 seconds total)