Starting phenix.real_space_refine on Thu Feb 22 03:47:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww5_21928/02_2024/6ww5_21928_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww5_21928/02_2024/6ww5_21928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww5_21928/02_2024/6ww5_21928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww5_21928/02_2024/6ww5_21928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww5_21928/02_2024/6ww5_21928_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww5_21928/02_2024/6ww5_21928_trim_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5984 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 74 5.16 5 C 8686 2.51 5 N 2166 2.21 5 O 2454 1.98 5 H 13425 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 28": "OD1" <-> "OD2" Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "B ASP 28": "OD1" <-> "OD2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "C ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "E ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 70": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D GLU 195": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26807 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6814 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6814 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3385 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 215} Chain: "E" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3384 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 215} Chain: "F" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3164 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Chain: "D" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3164 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'6PE': 1, 'HEX': 1, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'6PE': 1, 'HEX': 1, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.44, per 1000 atoms: 0.46 Number of scatterers: 26807 At special positions: 0 Unit cell: (113.058, 122.194, 138.182, 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) S 74 16.00 P 2 15.00 O 2454 8.00 N 2166 7.00 C 8686 6.00 H 13425 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 210 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " 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 Time building additional restraints: 26.55 Conformation dependent library (CDL) restraints added in 3.0 seconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 24 sheets defined 38.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 43 through 60 Processing helix chain 'A' and resid 66 through 78 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 93 removed outlier: 4.597A pdb=" N ASN A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.795A pdb=" N MET A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 145 removed outlier: 4.728A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.281A pdb=" N ILE A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 218 through 239 Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 311 through 317 Processing helix chain 'A' and resid 320 through 338 removed outlier: 3.942A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 378 through 395 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 410 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'B' and resid 20 through 38 Processing helix chain 'B' and resid 43 through 60 Processing helix chain 'B' and resid 66 through 78 Proline residue: B 74 - end of helix Processing helix chain 'B' and resid 85 through 93 removed outlier: 4.597A pdb=" N ASN B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 115 through 126 removed outlier: 3.794A pdb=" N MET B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 4.729A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 176 through 194 removed outlier: 4.281A pdb=" N ILE B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 218 through 239 Proline residue: B 223 - end of helix Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 320 through 338 removed outlier: 3.942A pdb=" N GLY B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 372 Processing helix chain 'B' and resid 378 through 395 Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 400 through 410 Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'F' and resid 122 through 124 No H-bonds generated for 'chain 'F' and resid 122 through 124' Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 183 through 187 Processing sheet with id= A, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.039A pdb=" N THR C 124 " --> pdb=" O VAL C 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 17 through 20 Processing sheet with id= D, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= E, first strand: chain 'C' and resid 149 through 156 Processing sheet with id= F, first strand: chain 'C' and resid 165 through 168 removed outlier: 3.554A pdb=" N SER C 167 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= H, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.037A pdb=" N THR E 124 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 17 through 20 Processing sheet with id= J, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= K, first strand: chain 'E' and resid 149 through 156 Processing sheet with id= L, first strand: chain 'E' and resid 165 through 168 removed outlier: 3.555A pdb=" N SER E 167 " --> pdb=" O ASN E 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 5 through 7 Processing sheet with id= N, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.272A pdb=" N LYS F 103 " --> pdb=" O LEU F 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 85 through 89 removed outlier: 3.665A pdb=" N ILE F 48 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 114 through 117 Processing sheet with id= Q, first strand: chain 'F' and resid 130 through 132 Processing sheet with id= R, first strand: chain 'F' and resid 147 through 149 Processing sheet with id= S, first strand: chain 'D' and resid 5 through 7 Processing sheet with id= T, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.272A pdb=" N LYS D 103 " --> pdb=" O LEU D 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 85 through 89 removed outlier: 3.666A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 114 through 117 Processing sheet with id= W, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= X, first strand: chain 'D' and resid 147 through 149 574 hydrogen bonds defined for protein. 1608 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: 10.67 Time building geometry restraints manager: 26.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 13419 1.01 - 1.21: 10 1.21 - 1.41: 5514 1.41 - 1.61: 8044 1.61 - 1.81: 130 Bond restraints: 27117 Sorted by residual: bond pdb=" CA ILE A 386 " pdb=" CB ILE A 386 " ideal model delta sigma weight residual 1.537 1.523 0.014 5.00e-03 4.00e+04 8.18e+00 bond pdb=" CA ILE B 386 " pdb=" CB ILE B 386 " ideal model delta sigma weight residual 1.537 1.523 0.014 5.00e-03 4.00e+04 8.09e+00 bond pdb=" CG LEU D 46 " pdb=" CD2 LEU D 46 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.08e+00 bond pdb=" CG LEU F 46 " pdb=" CD2 LEU F 46 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.01e+00 bond pdb=" ND2 ASN B 44 " pdb="HD22 ASN B 44 " ideal model delta sigma weight residual 0.860 0.806 0.054 2.00e-02 2.50e+03 7.41e+00 ... (remaining 27112 not shown) Histogram of bond angle deviations from ideal: 77.13 - 88.53: 7 88.53 - 99.93: 19 99.93 - 111.33: 30347 111.33 - 122.72: 15259 122.72 - 134.12: 3368 Bond angle restraints: 49000 Sorted by residual: angle pdb=" SD MET B 147 " pdb=" CE MET B 147 " pdb=" HE2 MET B 147 " ideal model delta sigma weight residual 109.00 77.13 31.87 3.00e+00 1.11e-01 1.13e+02 angle pdb=" SD MET B 147 " pdb=" CE MET B 147 " pdb=" HE3 MET B 147 " ideal model delta sigma weight residual 109.00 77.21 31.79 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CB LEU A 58 " pdb=" CG LEU A 58 " pdb=" HG LEU A 58 " ideal model delta sigma weight residual 109.00 77.48 31.52 3.00e+00 1.11e-01 1.10e+02 angle pdb=" CD2 LEU A 58 " pdb=" CG LEU A 58 " pdb=" HG LEU A 58 " ideal model delta sigma weight residual 108.00 77.25 30.75 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CD1 LEU A 58 " pdb=" CG LEU A 58 " pdb=" HG LEU A 58 " ideal model delta sigma weight residual 108.00 78.01 29.99 3.00e+00 1.11e-01 9.99e+01 ... (remaining 48995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 12387 31.93 - 63.85: 523 63.85 - 95.78: 25 95.78 - 127.71: 0 127.71 - 159.64: 2 Dihedral angle restraints: 12937 sinusoidal: 6856 harmonic: 6081 Sorted by residual: dihedral pdb=" CA PHE C 160 " pdb=" C PHE C 160 " pdb=" N PRO C 161 " pdb=" CA PRO C 161 " ideal model delta harmonic sigma weight residual -180.00 -124.76 -55.24 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA PHE E 160 " pdb=" C PHE E 160 " pdb=" N PRO E 161 " pdb=" CA PRO E 161 " ideal model delta harmonic sigma weight residual -180.00 -124.77 -55.23 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA TYR F 140 " pdb=" C TYR F 140 " pdb=" N PRO F 141 " pdb=" CA PRO F 141 " ideal model delta harmonic sigma weight residual -180.00 -126.40 -53.60 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 12934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2165 0.151 - 0.303: 29 0.303 - 0.454: 2 0.454 - 0.605: 0 0.605 - 0.756: 2 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CG LEU B 58 " pdb=" CB LEU B 58 " pdb=" CD1 LEU B 58 " pdb=" CD2 LEU B 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CB ILE E 129 " pdb=" CA ILE E 129 " pdb=" CG1 ILE E 129 " pdb=" CG2 ILE E 129 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 2195 not shown) Planarity restraints: 3988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 288 " -0.046 2.00e-02 2.50e+03 4.24e-02 5.40e+01 pdb=" CG PHE B 288 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE B 288 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 288 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE B 288 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 288 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 288 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE B 288 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE B 288 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE B 288 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE B 288 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE B 288 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 288 " -0.045 2.00e-02 2.50e+03 4.20e-02 5.30e+01 pdb=" CG PHE A 288 " 0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE A 288 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 288 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 PHE A 288 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 288 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE A 288 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 288 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 288 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 288 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 288 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 288 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 80 " -0.050 2.00e-02 2.50e+03 4.03e-02 4.87e+01 pdb=" CG PHE B 80 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE B 80 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 80 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE B 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 80 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 80 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE B 80 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 80 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE B 80 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE B 80 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE B 80 " -0.002 2.00e-02 2.50e+03 ... (remaining 3985 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 703 2.07 - 2.70: 45759 2.70 - 3.33: 78284 3.33 - 3.97: 103034 3.97 - 4.60: 163059 Nonbonded interactions: 390839 Sorted by model distance: nonbonded pdb=" O SER B 350 " pdb=" HH TYR D 92 " model vdw 1.434 1.850 nonbonded pdb=" O ILE A 191 " pdb=" H ILE A 194 " model vdw 1.521 1.850 nonbonded pdb=" O ILE B 191 " pdb=" H ILE B 194 " model vdw 1.522 1.850 nonbonded pdb=" O TRP B 461 " pdb="HH21 ARG D 66 " model vdw 1.543 1.850 nonbonded pdb=" HE ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 1.559 1.850 ... (remaining 390834 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 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 101 or (resid 102 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 103 through 228)) selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.380 Extract box with map and model: 5.120 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 95.050 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.094 13692 Z= 0.841 Angle : 0.980 13.492 18630 Z= 0.492 Chirality : 0.063 0.756 2198 Planarity : 0.008 0.138 2304 Dihedral : 16.537 159.637 4760 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.56 % Favored : 88.87 % Rotamer: Outliers : 1.52 % Allowed : 1.38 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.36 % 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: -2.89 (0.18), residues: 1752 helix: -0.92 (0.18), residues: 730 sheet: -2.07 (0.24), residues: 376 loop : -2.85 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 106 HIS 0.031 0.003 HIS C 35 PHE 0.118 0.007 PHE A 288 TYR 0.089 0.005 TYR D 55 ARG 0.027 0.002 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.994 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.7693 (mmt) cc_final: 0.7489 (mmm) REVERT: B 94 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7704 (t0) REVERT: B 158 MET cc_start: 0.7981 (mmt) cc_final: 0.7555 (mmm) REVERT: E 223 LYS cc_start: 0.5895 (mmmt) cc_final: 0.5228 (mmtm) REVERT: D 185 ASP cc_start: 0.6939 (m-30) cc_final: 0.6661 (m-30) outliers start: 22 outliers final: 4 residues processed: 173 average time/residue: 0.5307 time to fit residues: 136.5863 Evaluate side-chains 143 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 94 ASN A 203 ASN B 44 ASN B 94 ASN B 203 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 199 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13692 Z= 0.225 Angle : 0.665 12.567 18630 Z= 0.333 Chirality : 0.055 1.686 2198 Planarity : 0.007 0.141 2304 Dihedral : 9.149 140.232 1924 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.76 % Favored : 91.89 % Rotamer: Outliers : 1.31 % Allowed : 6.92 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.24 % 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 (0.20), residues: 1752 helix: -0.16 (0.19), residues: 732 sheet: -1.81 (0.24), residues: 396 loop : -2.57 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.005 0.001 HIS E 35 PHE 0.023 0.002 PHE B 80 TYR 0.018 0.002 TYR D 55 ARG 0.007 0.001 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 2.126 Fit side-chains REVERT: B 226 MET cc_start: 0.7858 (mtm) cc_final: 0.7599 (mtm) REVERT: C 89 GLU cc_start: 0.7471 (mp0) cc_final: 0.7015 (pp20) REVERT: C 90 ASP cc_start: 0.7795 (m-30) cc_final: 0.7398 (m-30) REVERT: E 89 GLU cc_start: 0.7400 (mp0) cc_final: 0.7069 (pp20) REVERT: E 223 LYS cc_start: 0.5919 (mmmt) cc_final: 0.5223 (mmtm) REVERT: F 118 PHE cc_start: 0.6590 (m-10) cc_final: 0.6190 (m-10) outliers start: 19 outliers final: 12 residues processed: 160 average time/residue: 0.5425 time to fit residues: 132.2697 Evaluate side-chains 152 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13692 Z= 0.378 Angle : 0.681 11.242 18630 Z= 0.350 Chirality : 0.056 1.684 2198 Planarity : 0.007 0.137 2304 Dihedral : 9.112 140.270 1924 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.85 % Favored : 90.70 % Rotamer: Outliers : 1.73 % Allowed : 8.58 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1752 helix: -0.09 (0.19), residues: 732 sheet: -1.77 (0.25), residues: 394 loop : -2.34 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 106 HIS 0.005 0.001 HIS B 112 PHE 0.022 0.002 PHE E 160 TYR 0.012 0.002 TYR F 49 ARG 0.004 0.001 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 2.017 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.7811 (ptm) cc_final: 0.7286 (ptm) REVERT: B 157 MET cc_start: 0.7842 (ptm) cc_final: 0.7292 (ptm) REVERT: C 89 GLU cc_start: 0.7742 (mp0) cc_final: 0.7334 (pp20) REVERT: E 89 GLU cc_start: 0.7511 (mp0) cc_final: 0.7131 (pp20) REVERT: E 90 ASP cc_start: 0.8184 (m-30) cc_final: 0.7964 (m-30) REVERT: E 223 LYS cc_start: 0.5877 (mmmt) cc_final: 0.5157 (mmtm) REVERT: F 118 PHE cc_start: 0.6639 (m-10) cc_final: 0.5830 (m-10) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.5025 time to fit residues: 125.8981 Evaluate side-chains 168 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13692 Z= 0.246 Angle : 0.609 10.850 18630 Z= 0.309 Chirality : 0.054 1.693 2198 Planarity : 0.007 0.135 2304 Dihedral : 8.855 141.283 1920 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.42 % Favored : 92.35 % Rotamer: Outliers : 1.87 % Allowed : 10.93 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1752 helix: 0.13 (0.20), residues: 732 sheet: -1.67 (0.25), residues: 412 loop : -2.29 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 PHE 0.019 0.001 PHE C 160 TYR 0.011 0.001 TYR F 36 ARG 0.002 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 2.005 Fit side-chains REVERT: B 226 MET cc_start: 0.7972 (mtm) cc_final: 0.7666 (mtm) REVERT: C 89 GLU cc_start: 0.7567 (mp0) cc_final: 0.7322 (mp0) REVERT: E 89 GLU cc_start: 0.7424 (mp0) cc_final: 0.7026 (mp0) REVERT: E 90 ASP cc_start: 0.8178 (m-30) cc_final: 0.7934 (m-30) REVERT: E 223 LYS cc_start: 0.5770 (mmmt) cc_final: 0.5167 (mmtm) REVERT: F 90 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: F 118 PHE cc_start: 0.6688 (m-10) cc_final: 0.5862 (m-10) outliers start: 27 outliers final: 23 residues processed: 163 average time/residue: 0.5140 time to fit residues: 127.2734 Evaluate side-chains 169 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13692 Z= 0.232 Angle : 0.590 10.698 18630 Z= 0.299 Chirality : 0.054 1.686 2198 Planarity : 0.007 0.134 2304 Dihedral : 8.674 141.516 1920 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.71 % Favored : 92.01 % Rotamer: Outliers : 2.21 % Allowed : 11.62 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1752 helix: 0.30 (0.20), residues: 734 sheet: -1.58 (0.25), residues: 410 loop : -2.14 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 PHE 0.018 0.001 PHE E 160 TYR 0.010 0.001 TYR F 36 ARG 0.005 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 2.063 Fit side-chains REVERT: A 459 LEU cc_start: 0.7300 (mp) cc_final: 0.6900 (tt) REVERT: B 157 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7784 (ptm) REVERT: B 226 MET cc_start: 0.7927 (mtm) cc_final: 0.7622 (mtm) REVERT: C 78 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6408 (p) REVERT: C 89 GLU cc_start: 0.7574 (mp0) cc_final: 0.7352 (mp0) REVERT: E 78 THR cc_start: 0.6587 (OUTLIER) cc_final: 0.6310 (p) REVERT: E 89 GLU cc_start: 0.7455 (mp0) cc_final: 0.7069 (mp0) REVERT: E 90 ASP cc_start: 0.8171 (m-30) cc_final: 0.7923 (m-30) REVERT: E 223 LYS cc_start: 0.5778 (mmmt) cc_final: 0.5117 (mmtm) REVERT: F 118 PHE cc_start: 0.6698 (m-10) cc_final: 0.5917 (m-10) REVERT: F 133 VAL cc_start: 0.6299 (t) cc_final: 0.6093 (t) REVERT: F 182 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7375 (p) outliers start: 32 outliers final: 20 residues processed: 171 average time/residue: 0.5463 time to fit residues: 141.2189 Evaluate side-chains 173 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN D 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13692 Z= 0.244 Angle : 0.586 10.723 18630 Z= 0.298 Chirality : 0.054 1.691 2198 Planarity : 0.007 0.133 2304 Dihedral : 8.623 141.927 1919 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.59 % Favored : 92.12 % Rotamer: Outliers : 2.56 % Allowed : 12.24 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1752 helix: 0.43 (0.20), residues: 728 sheet: -1.42 (0.25), residues: 394 loop : -1.96 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 PHE 0.019 0.001 PHE C 160 TYR 0.010 0.001 TYR D 49 ARG 0.002 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: A 459 LEU cc_start: 0.7186 (mp) cc_final: 0.6805 (tt) REVERT: B 94 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7728 (t0) REVERT: B 157 MET cc_start: 0.8216 (ptm) cc_final: 0.7832 (ptm) REVERT: B 226 MET cc_start: 0.8014 (mtm) cc_final: 0.7715 (mtm) REVERT: B 459 LEU cc_start: 0.7248 (mp) cc_final: 0.6851 (tt) REVERT: C 78 THR cc_start: 0.6775 (OUTLIER) cc_final: 0.6437 (p) REVERT: C 89 GLU cc_start: 0.7541 (mp0) cc_final: 0.7312 (mp0) REVERT: C 129 ILE cc_start: 0.3615 (OUTLIER) cc_final: 0.2700 (tp) REVERT: E 78 THR cc_start: 0.6584 (OUTLIER) cc_final: 0.6329 (p) REVERT: E 89 GLU cc_start: 0.7578 (mp0) cc_final: 0.7201 (pp20) REVERT: E 90 ASP cc_start: 0.8178 (m-30) cc_final: 0.7956 (m-30) REVERT: E 223 LYS cc_start: 0.5908 (mmmt) cc_final: 0.5288 (mmtm) REVERT: F 118 PHE cc_start: 0.6717 (m-10) cc_final: 0.5929 (m-10) outliers start: 37 outliers final: 27 residues processed: 182 average time/residue: 0.5806 time to fit residues: 156.8345 Evaluate side-chains 183 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13692 Z= 0.194 Angle : 0.564 10.751 18630 Z= 0.284 Chirality : 0.053 1.681 2198 Planarity : 0.007 0.133 2304 Dihedral : 8.513 142.636 1919 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.31 % Favored : 92.47 % Rotamer: Outliers : 2.01 % Allowed : 13.62 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1752 helix: 0.57 (0.20), residues: 728 sheet: -1.33 (0.25), residues: 392 loop : -1.88 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 PHE 0.020 0.001 PHE E 160 TYR 0.009 0.001 TYR F 36 ARG 0.003 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7667 (t0) REVERT: A 459 LEU cc_start: 0.7246 (mp) cc_final: 0.6889 (tt) REVERT: B 94 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 157 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7860 (ptm) REVERT: B 226 MET cc_start: 0.8000 (mtm) cc_final: 0.7671 (mtm) REVERT: B 459 LEU cc_start: 0.7237 (mp) cc_final: 0.6869 (tt) REVERT: C 78 THR cc_start: 0.6713 (OUTLIER) cc_final: 0.6364 (p) REVERT: C 89 GLU cc_start: 0.7522 (mp0) cc_final: 0.7309 (mp0) REVERT: E 78 THR cc_start: 0.6569 (OUTLIER) cc_final: 0.6273 (p) REVERT: E 89 GLU cc_start: 0.7536 (mp0) cc_final: 0.7230 (pp20) REVERT: E 90 ASP cc_start: 0.8159 (m-30) cc_final: 0.7939 (m-30) REVERT: E 223 LYS cc_start: 0.5876 (mmmt) cc_final: 0.5164 (mmtm) REVERT: F 118 PHE cc_start: 0.6721 (m-10) cc_final: 0.5939 (m-10) outliers start: 29 outliers final: 18 residues processed: 169 average time/residue: 0.5763 time to fit residues: 142.9606 Evaluate side-chains 171 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 0.0020 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 150 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13692 Z= 0.214 Angle : 0.565 10.741 18630 Z= 0.286 Chirality : 0.054 1.685 2198 Planarity : 0.007 0.132 2304 Dihedral : 8.453 141.954 1919 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.42 % Favored : 92.29 % Rotamer: Outliers : 2.28 % Allowed : 13.90 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1752 helix: 0.63 (0.20), residues: 728 sheet: -1.24 (0.26), residues: 382 loop : -1.94 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.004 0.001 HIS B 112 PHE 0.017 0.001 PHE E 160 TYR 0.008 0.001 TYR F 36 ARG 0.003 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7798 (t0) REVERT: A 459 LEU cc_start: 0.7250 (mp) cc_final: 0.6900 (tt) REVERT: B 94 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7810 (t0) REVERT: B 157 MET cc_start: 0.8247 (ptm) cc_final: 0.7846 (ptm) REVERT: B 226 MET cc_start: 0.8000 (mtm) cc_final: 0.7677 (mtm) REVERT: B 459 LEU cc_start: 0.7244 (mp) cc_final: 0.6885 (tt) REVERT: C 78 THR cc_start: 0.6719 (OUTLIER) cc_final: 0.6377 (p) REVERT: C 89 GLU cc_start: 0.7551 (mp0) cc_final: 0.7289 (mp0) REVERT: E 78 THR cc_start: 0.6617 (OUTLIER) cc_final: 0.6287 (p) REVERT: E 89 GLU cc_start: 0.7535 (mp0) cc_final: 0.7213 (pp20) REVERT: E 90 ASP cc_start: 0.8158 (m-30) cc_final: 0.7939 (m-30) REVERT: E 223 LYS cc_start: 0.5827 (mmmt) cc_final: 0.5165 (mmtm) REVERT: F 118 PHE cc_start: 0.6729 (m-10) cc_final: 0.5948 (m-10) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.5684 time to fit residues: 146.5494 Evaluate side-chains 174 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 147 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN D 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13692 Z= 0.276 Angle : 0.592 10.768 18630 Z= 0.302 Chirality : 0.055 1.696 2198 Planarity : 0.007 0.132 2304 Dihedral : 8.570 142.322 1918 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.11 % Favored : 91.55 % Rotamer: Outliers : 2.14 % Allowed : 14.32 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1752 helix: 0.53 (0.20), residues: 728 sheet: -1.11 (0.27), residues: 362 loop : -1.82 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS B 112 PHE 0.017 0.001 PHE E 160 TYR 0.009 0.001 TYR F 36 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 2.502 Fit side-chains revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7871 (t0) REVERT: A 459 LEU cc_start: 0.7208 (mp) cc_final: 0.6848 (tt) REVERT: B 94 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7874 (t0) REVERT: B 157 MET cc_start: 0.8252 (ptm) cc_final: 0.7827 (ptm) REVERT: B 226 MET cc_start: 0.8021 (mtm) cc_final: 0.7735 (mtm) REVERT: B 459 LEU cc_start: 0.7189 (mp) cc_final: 0.6822 (tt) REVERT: C 78 THR cc_start: 0.6821 (OUTLIER) cc_final: 0.6492 (p) REVERT: C 89 GLU cc_start: 0.7561 (mp0) cc_final: 0.7340 (mp0) REVERT: E 78 THR cc_start: 0.6715 (OUTLIER) cc_final: 0.6396 (p) REVERT: E 89 GLU cc_start: 0.7580 (mp0) cc_final: 0.7210 (pp20) REVERT: E 90 ASP cc_start: 0.8196 (m-30) cc_final: 0.7982 (m-30) REVERT: E 223 LYS cc_start: 0.5855 (mmmt) cc_final: 0.5186 (mmtm) REVERT: F 118 PHE cc_start: 0.6757 (m-10) cc_final: 0.5950 (m-10) outliers start: 31 outliers final: 25 residues processed: 170 average time/residue: 0.5871 time to fit residues: 145.9281 Evaluate side-chains 172 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 136 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13692 Z= 0.201 Angle : 0.563 10.755 18630 Z= 0.285 Chirality : 0.053 1.675 2198 Planarity : 0.006 0.132 2304 Dihedral : 8.499 143.363 1918 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.25 % Favored : 92.52 % Rotamer: Outliers : 1.73 % Allowed : 14.94 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1752 helix: 0.67 (0.20), residues: 728 sheet: -1.14 (0.27), residues: 372 loop : -1.80 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 PHE 0.016 0.001 PHE E 160 TYR 0.009 0.001 TYR F 36 ARG 0.003 0.000 ARG B 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LEU cc_start: 0.7214 (mp) cc_final: 0.6877 (tt) REVERT: B 157 MET cc_start: 0.8209 (ptm) cc_final: 0.7746 (ptm) REVERT: B 226 MET cc_start: 0.8065 (mtm) cc_final: 0.7450 (mtm) REVERT: B 428 PHE cc_start: 0.8233 (t80) cc_final: 0.7953 (t80) REVERT: B 459 LEU cc_start: 0.7249 (mp) cc_final: 0.6884 (tt) REVERT: C 78 THR cc_start: 0.6731 (OUTLIER) cc_final: 0.6389 (p) REVERT: C 89 GLU cc_start: 0.7503 (mp0) cc_final: 0.7292 (mp0) REVERT: E 78 THR cc_start: 0.6625 (OUTLIER) cc_final: 0.6280 (p) REVERT: E 89 GLU cc_start: 0.7501 (mp0) cc_final: 0.7208 (pp20) REVERT: E 90 ASP cc_start: 0.8154 (m-30) cc_final: 0.7934 (m-30) REVERT: E 223 LYS cc_start: 0.5850 (mmmt) cc_final: 0.5183 (mmtm) REVERT: F 118 PHE cc_start: 0.6790 (m-10) cc_final: 0.6004 (m-10) outliers start: 25 outliers final: 22 residues processed: 162 average time/residue: 0.5951 time to fit residues: 141.0269 Evaluate side-chains 168 residues out of total 1450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 70 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 136 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.171365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124770 restraints weight = 41667.061| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.80 r_work: 0.3375 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13692 Z= 0.214 Angle : 0.562 10.720 18630 Z= 0.285 Chirality : 0.053 1.677 2198 Planarity : 0.006 0.132 2304 Dihedral : 8.358 142.656 1914 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.36 % Favored : 92.35 % Rotamer: Outliers : 1.66 % Allowed : 15.08 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.21), residues: 1752 helix: 0.72 (0.20), residues: 728 sheet: -1.19 (0.26), residues: 384 loop : -1.71 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 106 HIS 0.004 0.001 HIS B 112 PHE 0.015 0.001 PHE E 160 TYR 0.008 0.001 TYR F 36 ARG 0.003 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5718.65 seconds wall clock time: 102 minutes 42.45 seconds (6162.45 seconds total)