Starting phenix.real_space_refine on Wed Feb 14 12:40:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wur_32839/02_2024/7wur_32839.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wur_32839/02_2024/7wur_32839.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/7wur_32839/02_2024/7wur_32839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wur_32839/02_2024/7wur_32839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wur_32839/02_2024/7wur_32839.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wur_32839/02_2024/7wur_32839.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 ------------------------------------------------------------------------------- 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 336 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5636 2.51 5 N 1528 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 327": "OD1" <-> "OD2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1": "OE1" <-> "OE2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8922 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321} Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2725 Classifications: {'peptide': 341} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 321} Chain: "E" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "F" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "G" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Time building chain proxies: 4.78, per 1000 atoms: 0.54 Number of scatterers: 8922 At special positions: 0 Unit cell: (84.48, 109.56, 162.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1706 8.00 N 1528 7.00 C 5636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " 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: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 20 sheets defined 12.8% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.759A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 3.808A pdb=" N ASN A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Proline residue: A 73 - end of helix removed outlier: 3.637A pdb=" N HIS A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.592A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.501A pdb=" N ASN A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.675A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.749A pdb=" N ASN B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.552A pdb=" N HIS B 229 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.561A pdb=" N ASN B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.665A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.716A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.670A pdb=" N THR E 91 " --> pdb=" O ASP E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.841A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.815A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.822A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.899A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.598A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 removed outlier: 3.642A pdb=" N MET A 89 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.366A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 216 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 216 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA B 205 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE B 212 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 removed outlier: 5.996A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.563A pdb=" N MET B 89 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 5.990A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.089A pdb=" N TYR E 107 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY E 109 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS E 96 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY E 111 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TYR E 94 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU E 113 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA E 92 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.601A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.135A pdb=" N TYR G 107 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY G 109 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS G 96 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY G 111 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TYR G 94 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU G 113 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA G 92 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.680A pdb=" N PHE H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 19 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.680A pdb=" N PHE H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP H 71 " --> pdb=" O SER H 68 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.247A pdb=" N LEU H 11 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR H 87 " --> pdb=" O THR H 104 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 564 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: 2.65 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2870 1.34 - 1.46: 2341 1.46 - 1.58: 3867 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 9150 Sorted by residual: bond pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.44e+00 bond pdb=" CA ILE B 243 " pdb=" CB ILE B 243 " ideal model delta sigma weight residual 1.540 1.522 0.018 1.23e-02 6.61e+03 2.11e+00 bond pdb=" CB GLN A 70 " pdb=" CG GLN A 70 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.80e+00 bond pdb=" C PRO A 106 " pdb=" N GLN A 107 " ideal model delta sigma weight residual 1.329 1.347 -0.018 1.40e-02 5.10e+03 1.71e+00 ... (remaining 9145 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.98: 194 105.98 - 112.99: 4880 112.99 - 120.00: 3051 120.00 - 127.02: 4132 127.02 - 134.03: 153 Bond angle restraints: 12410 Sorted by residual: angle pdb=" C PRO B 106 " pdb=" N GLN B 107 " pdb=" CA GLN B 107 " ideal model delta sigma weight residual 121.70 133.13 -11.43 1.80e+00 3.09e-01 4.03e+01 angle pdb=" C PRO A 106 " pdb=" N GLN A 107 " pdb=" CA GLN A 107 " ideal model delta sigma weight residual 121.70 132.97 -11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" CB MET E 34 " pdb=" CG MET E 34 " pdb=" SD MET E 34 " ideal model delta sigma weight residual 112.70 125.95 -13.25 3.00e+00 1.11e-01 1.95e+01 angle pdb=" CA GLN A 70 " pdb=" CB GLN A 70 " pdb=" CG GLN A 70 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB MET B 198 " pdb=" CG MET B 198 " pdb=" SD MET B 198 " ideal model delta sigma weight residual 112.70 124.65 -11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 12405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4831 17.32 - 34.64: 478 34.64 - 51.97: 97 51.97 - 69.29: 6 69.29 - 86.61: 14 Dihedral angle restraints: 5426 sinusoidal: 2178 harmonic: 3248 Sorted by residual: dihedral pdb=" CA LYS A 33 " pdb=" C LYS A 33 " pdb=" N PHE A 34 " pdb=" CA PHE A 34 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 143 " pdb=" CB CYS B 143 " ideal model delta sinusoidal sigma weight residual -86.00 -123.21 37.21 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA LYS A 189 " pdb=" C LYS A 189 " pdb=" N ASP A 190 " pdb=" CA ASP A 190 " ideal model delta harmonic sigma weight residual 180.00 157.90 22.10 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 5423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1080 0.049 - 0.097: 177 0.097 - 0.146: 71 0.146 - 0.194: 0 0.194 - 0.243: 2 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA GLN A 107 " pdb=" N GLN A 107 " pdb=" C GLN A 107 " pdb=" CB GLN A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLN B 107 " pdb=" N GLN B 107 " pdb=" C GLN B 107 " pdb=" CB GLN B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA GLN E 110 " pdb=" N GLN E 110 " pdb=" C GLN E 110 " pdb=" CB GLN E 110 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1327 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.010 2.00e-02 2.50e+03 1.30e-02 2.96e+00 pdb=" CG PHE B 20 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 70 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C GLN A 70 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN A 70 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 71 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 72 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 73 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.020 5.00e-02 4.00e+02 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 925 2.75 - 3.29: 8826 3.29 - 3.82: 14527 3.82 - 4.36: 17416 4.36 - 4.90: 29740 Nonbonded interactions: 71434 Sorted by model distance: nonbonded pdb=" OE2 GLU A 281 " pdb=" OG SER E 52 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU B 281 " pdb=" OG SER G 52 " model vdw 2.222 2.440 nonbonded pdb=" OG1 THR A 288 " pdb=" OD1 ASP A 290 " model vdw 2.242 2.440 nonbonded pdb=" N GLU E 89 " pdb=" OE1 GLU E 89 " model vdw 2.245 2.520 nonbonded pdb=" OG SER B 103 " pdb=" OE1 GLN B 175 " model vdw 2.247 2.440 ... (remaining 71429 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 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 3.670 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.330 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.003 0.040 9150 Z= 0.177 Angle : 0.680 13.252 12410 Z= 0.386 Chirality : 0.043 0.243 1330 Planarity : 0.003 0.035 1578 Dihedral : 14.344 86.610 3306 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.31 % Allowed : 9.86 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.48 (0.26), residues: 1122 helix: -1.02 (0.57), residues: 68 sheet: -0.59 (0.29), residues: 360 loop : -1.20 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 108 HIS 0.001 0.000 HIS B 229 PHE 0.030 0.001 PHE B 20 TYR 0.011 0.001 TYR B 32 ARG 0.003 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.8624 (tpp) cc_final: 0.8311 (tpt) REVERT: A 333 MET cc_start: 0.8411 (mmm) cc_final: 0.7856 (mtt) REVERT: E 110 GLN cc_start: 0.8508 (mp10) cc_final: 0.7686 (pp30) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.2174 time to fit residues: 21.5610 Evaluate side-chains 67 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain F residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9150 Z= 0.212 Angle : 0.615 11.830 12410 Z= 0.324 Chirality : 0.043 0.247 1330 Planarity : 0.003 0.029 1578 Dihedral : 4.951 47.863 1237 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.72 % Allowed : 10.99 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.40 (0.26), residues: 1122 helix: -0.34 (0.59), residues: 72 sheet: -0.46 (0.29), residues: 350 loop : -1.27 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 108 HIS 0.003 0.001 HIS B 195 PHE 0.018 0.001 PHE B 34 TYR 0.010 0.001 TYR B 32 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: B 272 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8262 (ttm110) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 0.2046 time to fit residues: 20.8972 Evaluate side-chains 67 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 0.0020 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9150 Z= 0.192 Angle : 0.593 11.818 12410 Z= 0.310 Chirality : 0.042 0.244 1330 Planarity : 0.003 0.030 1578 Dihedral : 4.756 56.896 1233 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.03 % Allowed : 12.63 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.36 (0.26), residues: 1122 helix: 0.02 (0.61), residues: 72 sheet: -0.44 (0.29), residues: 348 loop : -1.27 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 108 HIS 0.003 0.001 HIS B 195 PHE 0.015 0.001 PHE A 34 TYR 0.009 0.001 TYR H 92 ARG 0.003 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9046 (pm20) cc_final: 0.8683 (pm20) REVERT: A 67 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7972 (tpp) REVERT: B 67 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8165 (tpp) REVERT: B 272 ARG cc_start: 0.8525 (mtt90) cc_final: 0.8210 (ttm110) REVERT: E 110 GLN cc_start: 0.8668 (mp10) cc_final: 0.7768 (pp30) REVERT: G 1 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7873 (tm-30) REVERT: G 3 GLN cc_start: 0.7896 (mp10) cc_final: 0.7617 (mp10) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 0.2131 time to fit residues: 22.7984 Evaluate side-chains 70 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9150 Z= 0.184 Angle : 0.591 11.801 12410 Z= 0.307 Chirality : 0.042 0.242 1330 Planarity : 0.003 0.028 1578 Dihedral : 4.692 54.161 1233 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.03 % Allowed : 13.66 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.29 (0.26), residues: 1122 helix: 0.18 (0.61), residues: 72 sheet: -0.50 (0.29), residues: 360 loop : -1.18 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.023 0.001 PHE A 34 TYR 0.010 0.001 TYR A 32 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.9005 (pm20) cc_final: 0.8666 (pm20) REVERT: A 67 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8216 (tpp) REVERT: A 68 TRP cc_start: 0.9405 (m100) cc_final: 0.9185 (m100) REVERT: B 67 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8203 (tmm) REVERT: B 272 ARG cc_start: 0.8479 (mtt90) cc_final: 0.8132 (ttm110) REVERT: G 1 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7943 (tm-30) REVERT: G 3 GLN cc_start: 0.7846 (mp10) cc_final: 0.7494 (mp10) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.2119 time to fit residues: 21.5509 Evaluate side-chains 74 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN B 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9150 Z= 0.175 Angle : 0.596 11.785 12410 Z= 0.308 Chirality : 0.042 0.241 1330 Planarity : 0.003 0.029 1578 Dihedral : 4.559 45.353 1233 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.44 % Allowed : 14.27 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.27 (0.26), residues: 1122 helix: 0.27 (0.61), residues: 72 sheet: -0.56 (0.29), residues: 364 loop : -1.12 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.012 0.001 PHE A 34 TYR 0.013 0.001 TYR A 32 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8992 (pm20) cc_final: 0.8675 (pm20) REVERT: A 67 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8189 (tpp) REVERT: B 67 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.7620 (tpp) REVERT: B 174 ARG cc_start: 0.8726 (ptp90) cc_final: 0.8155 (pmt-80) REVERT: B 272 ARG cc_start: 0.8487 (mtt90) cc_final: 0.8130 (ttm110) REVERT: E 110 GLN cc_start: 0.8535 (mp10) cc_final: 0.7761 (pp30) REVERT: F 79 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8649 (mm) REVERT: G 1 GLN cc_start: 0.8256 (tp-100) cc_final: 0.7990 (tm-30) REVERT: G 3 GLN cc_start: 0.7820 (mp10) cc_final: 0.7365 (mp10) outliers start: 14 outliers final: 5 residues processed: 78 average time/residue: 0.2224 time to fit residues: 25.1233 Evaluate side-chains 75 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 20.0000 chunk 95 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9150 Z= 0.175 Angle : 0.594 11.765 12410 Z= 0.306 Chirality : 0.043 0.240 1330 Planarity : 0.003 0.030 1578 Dihedral : 4.479 40.111 1233 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.23 % Allowed : 14.99 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.21 (0.26), residues: 1122 helix: 0.40 (0.61), residues: 72 sheet: -0.46 (0.29), residues: 360 loop : -1.13 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.002 0.001 HIS B 195 PHE 0.025 0.001 PHE B 20 TYR 0.015 0.001 TYR A 32 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: A 184 MET cc_start: 0.8369 (tpt) cc_final: 0.8169 (tpt) REVERT: B 174 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8258 (pmt-80) REVERT: B 241 MET cc_start: 0.8900 (mtp) cc_final: 0.8666 (mtp) REVERT: B 272 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8161 (ttm110) REVERT: F 61 ASP cc_start: 0.8802 (p0) cc_final: 0.8556 (t0) REVERT: F 79 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8698 (mm) REVERT: G 1 GLN cc_start: 0.8366 (tp-100) cc_final: 0.8135 (tm-30) REVERT: G 3 GLN cc_start: 0.7756 (mp10) cc_final: 0.7313 (mp10) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.2134 time to fit residues: 22.2755 Evaluate side-chains 76 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 20.0000 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9150 Z= 0.179 Angle : 0.607 11.755 12410 Z= 0.311 Chirality : 0.043 0.240 1330 Planarity : 0.003 0.033 1578 Dihedral : 4.265 29.014 1230 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.54 % Allowed : 15.20 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.15 (0.26), residues: 1122 helix: 0.51 (0.62), residues: 72 sheet: -0.48 (0.29), residues: 364 loop : -1.05 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 108 HIS 0.002 0.001 HIS B 195 PHE 0.012 0.001 PHE A 34 TYR 0.013 0.001 TYR A 32 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: B 174 ARG cc_start: 0.8733 (ptp90) cc_final: 0.8241 (pmt-80) REVERT: B 272 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8179 (ttm110) REVERT: E 110 GLN cc_start: 0.8434 (mp10) cc_final: 0.7850 (pp30) REVERT: F 61 ASP cc_start: 0.8898 (p0) cc_final: 0.8657 (t0) REVERT: F 79 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8705 (mm) REVERT: G 1 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8208 (tm-30) REVERT: G 3 GLN cc_start: 0.7651 (mp10) cc_final: 0.7206 (mp10) outliers start: 15 outliers final: 7 residues processed: 77 average time/residue: 0.2255 time to fit residues: 25.2633 Evaluate side-chains 75 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0980 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9150 Z= 0.148 Angle : 0.616 11.699 12410 Z= 0.309 Chirality : 0.043 0.239 1330 Planarity : 0.003 0.034 1578 Dihedral : 4.127 27.933 1230 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.44 % Allowed : 15.50 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % 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: -1.10 (0.26), residues: 1122 helix: 0.50 (0.61), residues: 72 sheet: -0.43 (0.29), residues: 364 loop : -1.03 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 108 HIS 0.003 0.000 HIS A 224 PHE 0.030 0.001 PHE B 20 TYR 0.011 0.001 TYR A 32 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: A 97 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8300 (mmt) REVERT: B 67 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.7404 (tpp) REVERT: B 174 ARG cc_start: 0.8720 (ptp90) cc_final: 0.8201 (pmt-80) REVERT: B 272 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8098 (ttm110) REVERT: E 110 GLN cc_start: 0.8264 (mp10) cc_final: 0.8023 (mp10) REVERT: F 61 ASP cc_start: 0.8933 (p0) cc_final: 0.8695 (t0) REVERT: F 79 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8650 (mm) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.2157 time to fit residues: 23.9238 Evaluate side-chains 77 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9150 Z= 0.249 Angle : 0.656 15.986 12410 Z= 0.329 Chirality : 0.043 0.240 1330 Planarity : 0.003 0.029 1578 Dihedral : 4.350 30.269 1230 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.44 % Allowed : 15.91 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.26), residues: 1122 helix: 0.99 (0.63), residues: 68 sheet: -0.39 (0.29), residues: 362 loop : -1.02 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 108 HIS 0.004 0.001 HIS A 224 PHE 0.026 0.001 PHE A 34 TYR 0.013 0.001 TYR A 32 ARG 0.002 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: B 47 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: B 174 ARG cc_start: 0.8755 (ptp90) cc_final: 0.8312 (pmt-80) REVERT: B 241 MET cc_start: 0.9093 (mtp) cc_final: 0.8849 (mtt) REVERT: B 272 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8187 (ttm110) REVERT: E 110 GLN cc_start: 0.8418 (mp10) cc_final: 0.8174 (mp10) REVERT: F 61 ASP cc_start: 0.8951 (p0) cc_final: 0.8657 (t0) REVERT: F 79 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8572 (mm) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 0.2148 time to fit residues: 22.8117 Evaluate side-chains 75 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.0030 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9150 Z= 0.320 Angle : 0.715 18.787 12410 Z= 0.358 Chirality : 0.044 0.243 1330 Planarity : 0.003 0.026 1578 Dihedral : 4.744 32.475 1230 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 1.33 % Allowed : 16.02 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1122 helix: 1.06 (0.64), residues: 68 sheet: -0.55 (0.29), residues: 342 loop : -1.03 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 68 HIS 0.004 0.001 HIS B 195 PHE 0.031 0.002 PHE B 20 TYR 0.015 0.001 TYR H 87 ARG 0.003 0.000 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8672 (pm20) REVERT: B 47 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: B 67 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7003 (tpp) REVERT: B 123 MET cc_start: 0.8582 (tpt) cc_final: 0.7937 (tpp) REVERT: B 272 ARG cc_start: 0.8663 (mtt90) cc_final: 0.8323 (ttm110) REVERT: E 59 ASP cc_start: 0.8549 (t0) cc_final: 0.8236 (t0) REVERT: E 100 TYR cc_start: 0.7904 (t80) cc_final: 0.7647 (t80) REVERT: E 110 GLN cc_start: 0.8562 (mp10) cc_final: 0.7832 (pp30) REVERT: F 61 ASP cc_start: 0.8899 (p0) cc_final: 0.8636 (t0) REVERT: F 79 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8593 (mm) outliers start: 13 outliers final: 6 residues processed: 71 average time/residue: 0.2115 time to fit residues: 21.6884 Evaluate side-chains 73 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.061040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043999 restraints weight = 42389.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045478 restraints weight = 20719.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046433 restraints weight = 13840.056| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9150 Z= 0.344 Angle : 0.730 20.413 12410 Z= 0.366 Chirality : 0.045 0.245 1330 Planarity : 0.003 0.030 1578 Dihedral : 4.883 34.014 1230 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.23 % Allowed : 16.43 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.26), residues: 1122 helix: 1.05 (0.64), residues: 68 sheet: -0.47 (0.29), residues: 330 loop : -1.14 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 68 HIS 0.005 0.001 HIS B 195 PHE 0.021 0.001 PHE A 34 TYR 0.012 0.001 TYR H 87 ARG 0.010 0.000 ARG B 174 =============================================================================== Job complete usr+sys time: 1723.21 seconds wall clock time: 32 minutes 34.33 seconds (1954.33 seconds total)