Starting phenix.real_space_refine on Mon Aug 5 18:27:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnp_37670/08_2024/8wnp_37670.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnp_37670/08_2024/8wnp_37670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnp_37670/08_2024/8wnp_37670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnp_37670/08_2024/8wnp_37670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnp_37670/08_2024/8wnp_37670.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wnp_37670/08_2024/8wnp_37670.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 8848 2.51 5 N 2444 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "E ARG 14": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 211": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 257": "NH1" <-> "NH2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E ARG 294": "NH1" <-> "NH2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 347": "NH1" <-> "NH2" Residue "F ARG 14": "NH1" <-> "NH2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F ARG 276": "NH1" <-> "NH2" Residue "F ARG 294": "NH1" <-> "NH2" Residue "F ARG 299": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 324": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 347": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G ARG 30": "NH1" <-> "NH2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 52": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 52": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14142 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1673 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 212} Chain: "C" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1673 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2818 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 923 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.67, per 1000 atoms: 0.75 Number of scatterers: 14142 At special positions: 0 Unit cell: (86.36, 155.72, 138.04, 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 74 16.00 O 2776 8.00 N 2444 7.00 C 8848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 215 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 215 " - pdb=" SG CYS D 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 4 " distance=2.05 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 179 " - pdb=" SG CYS E 223 " distance=2.04 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 312 " distance=2.04 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 15 " distance=2.05 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 143 " distance=2.03 Simple disulfide: pdb=" SG CYS F 179 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 312 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 316 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 401 " - " ASN E 207 " Time building additional restraints: 5.01 Conformation dependent library (CDL) restraints added in 2.7 seconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 37 sheets defined 10.0% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 122 through 128 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.525A pdb=" N GLU A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 204 through 207 Processing helix chain 'C' and resid 122 through 128 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.565A pdb=" N ASN D 33 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 130 through 134 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.806A pdb=" N GLY D 193 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'E' and resid 38 through 51 removed outlier: 3.726A pdb=" N GLU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 82 removed outlier: 3.639A pdb=" N SER E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 72 " --> pdb=" O TRP E 68 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.564A pdb=" N LEU E 241 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 248 removed outlier: 3.563A pdb=" N ALA E 248 " --> pdb=" O LYS E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 52 removed outlier: 3.668A pdb=" N GLU F 52 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 71 through 80 removed outlier: 3.777A pdb=" N LEU F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.623A pdb=" N HIS F 229 " --> pdb=" O PRO F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.677A pdb=" N LEU F 241 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'G' and resid 27 through 31 removed outlier: 3.979A pdb=" N ARG G 30 " --> pdb=" O THR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'H' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 4.304A pdb=" N VAL A 20 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 76 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS A 24 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 72 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.713A pdb=" N LEU A 12 " --> pdb=" O GLU A 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.932A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 86 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.594A pdb=" N ASN A 139 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR A 174 " --> pdb=" O ASN A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.608A pdb=" N LYS A 146 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.156A pdb=" N GLY B 11 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 92 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP B 99 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR B 34 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP B 37 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 50 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG B 39 " --> pdb=" O TRP B 48 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TRP B 48 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.664A pdb=" N VAL B 145 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 184 " --> pdb=" O HIS B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.664A pdb=" N VAL B 145 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157 removed outlier: 4.702A pdb=" N TYR B 197 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 7 through 8 removed outlier: 3.526A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS C 24 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.545A pdb=" N LEU C 12 " --> pdb=" O GLU C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.639A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.594A pdb=" N LEU C 136 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 134 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.526A pdb=" N VAL C 206 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.000A pdb=" N GLN D 4 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 26 " --> pdb=" O GLN D 4 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.703A pdb=" N ALA D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D 34 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET D 35 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL D 51 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.703A pdb=" N ALA D 92 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR D 105 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.738A pdb=" N GLY D 142 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 145 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 179 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 123 through 127 removed outlier: 3.738A pdb=" N GLY D 142 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 145 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 179 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 154 through 157 Processing sheet with id=AC4, first strand: chain 'E' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'E' and resid 32 through 34 removed outlier: 7.890A pdb=" N LYS E 33 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N LEU E 169 " --> pdb=" O LYS E 33 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TRP E 168 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 156 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.336A pdb=" N GLY E 56 " --> pdb=" O ALA E 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.760A pdb=" N THR E 87 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 135 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL E 89 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 329 through 331 removed outlier: 3.597A pdb=" N SER E 322 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU E 203 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 215 " --> pdb=" O TRP E 201 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP E 201 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 192 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP F 201 " --> pdb=" O HIS F 216 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU F 205 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU F 212 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N LYS F 213 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE F 277 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 311 through 312 Processing sheet with id=AD1, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.725A pdb=" N GLY F 3 " --> pdb=" O GLY F 16 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG F 14 " --> pdb=" O SER F 5 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 33 through 36 removed outlier: 3.557A pdb=" N LEU F 169 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 157 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS F 170 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL F 155 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 88 through 90 removed outlier: 6.391A pdb=" N VAL F 89 " --> pdb=" O VAL F 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 284 through 285 removed outlier: 5.940A pdb=" N LYS F 284 " --> pdb=" O TRP F 311 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.608A pdb=" N SER G 6 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.739A pdb=" N VAL G 11 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ARG G 37 " --> pdb=" O PHE G 46 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N PHE G 46 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.739A pdb=" N VAL G 11 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N CYS G 95 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP G 110 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE G 97 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.517A pdb=" N GLY H 9 " --> pdb=" O THR H 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.448A pdb=" N PHE H 46 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG H 37 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR H 109 " --> pdb=" O ILE H 97 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1077 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: 5.01 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 14374 1.57 - 1.93: 100 1.93 - 2.28: 0 2.28 - 2.63: 0 2.63 - 2.99: 3 Bond restraints: 14477 Sorted by residual: bond pdb=" C THR B 119 " pdb=" N LYS B 120 " ideal model delta sigma weight residual 1.332 2.916 -1.584 1.31e-02 5.83e+03 1.46e+04 bond pdb=" C THR D 119 " pdb=" N LYS D 120 " ideal model delta sigma weight residual 1.332 2.976 -1.644 1.40e-02 5.10e+03 1.38e+04 bond pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 1.327 2.987 -1.660 1.47e-02 4.63e+03 1.27e+04 bond pdb=" CA LEU B 127 " pdb=" CB LEU B 127 " ideal model delta sigma weight residual 1.525 1.552 -0.027 1.47e-02 4.63e+03 3.48e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 ... (remaining 14472 not shown) Histogram of bond angle deviations from ideal: 42.09 - 63.86: 2 63.86 - 85.62: 0 85.62 - 107.39: 566 107.39 - 129.15: 18946 129.15 - 150.92: 135 Bond angle restraints: 19649 Sorted by residual: angle pdb=" O THR D 119 " pdb=" C THR D 119 " pdb=" N LYS D 120 " ideal model delta sigma weight residual 122.59 42.09 80.50 1.33e+00 5.65e-01 3.66e+03 angle pdb=" O ARG A 109 " pdb=" C ARG A 109 " pdb=" N THR A 110 " ideal model delta sigma weight residual 122.59 57.99 64.60 1.33e+00 5.65e-01 2.36e+03 angle pdb=" CA THR B 119 " pdb=" C THR B 119 " pdb=" N LYS B 120 " ideal model delta sigma weight residual 116.39 86.00 30.39 1.26e+00 6.30e-01 5.82e+02 angle pdb=" C THR B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta sigma weight residual 122.95 150.92 -27.97 1.44e+00 4.82e-01 3.77e+02 angle pdb=" C THR D 119 " pdb=" N LYS D 120 " pdb=" CA LYS D 120 " ideal model delta sigma weight residual 121.54 102.63 18.91 1.91e+00 2.74e-01 9.81e+01 ... (remaining 19644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7800 17.91 - 35.81: 699 35.81 - 53.71: 154 53.71 - 71.62: 29 71.62 - 89.52: 17 Dihedral angle restraints: 8699 sinusoidal: 3466 harmonic: 5233 Sorted by residual: dihedral pdb=" CB CYS E 313 " pdb=" SG CYS E 313 " pdb=" SG CYS E 316 " pdb=" CB CYS E 316 " ideal model delta sinusoidal sigma weight residual -86.00 -170.54 84.54 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS F 313 " pdb=" SG CYS F 313 " pdb=" SG CYS F 316 " pdb=" CB CYS F 316 " ideal model delta sinusoidal sigma weight residual -86.00 -152.81 66.81 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CA ARG A 109 " pdb=" C ARG A 109 " pdb=" N THR A 110 " pdb=" CA THR A 110 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.73e+01 ... (remaining 8696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1559 0.039 - 0.078: 383 0.078 - 0.117: 148 0.117 - 0.156: 47 0.156 - 0.194: 2 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CA PRO E 320 " pdb=" N PRO E 320 " pdb=" C PRO E 320 " pdb=" CB PRO E 320 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA ILE E 21 " pdb=" N ILE E 21 " pdb=" C ILE E 21 " pdb=" CB ILE E 21 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE A 49 " pdb=" N ILE A 49 " pdb=" C ILE A 49 " pdb=" CB ILE A 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.71e-01 ... (remaining 2136 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 109 " -0.182 2.00e-02 2.50e+03 2.73e-01 7.44e+02 pdb=" C ARG A 109 " 0.438 2.00e-02 2.50e+03 pdb=" O ARG A 109 " -0.269 2.00e-02 2.50e+03 pdb=" N THR A 110 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 119 " 0.145 2.00e-02 2.50e+03 2.59e-01 6.69e+02 pdb=" C THR D 119 " -0.396 2.00e-02 2.50e+03 pdb=" O THR D 119 " 0.296 2.00e-02 2.50e+03 pdb=" N LYS D 120 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 119 " -0.082 2.00e-02 2.50e+03 1.76e-01 3.10e+02 pdb=" C THR B 119 " 0.296 2.00e-02 2.50e+03 pdb=" O THR B 119 " -0.165 2.00e-02 2.50e+03 pdb=" N LYS B 120 " -0.048 2.00e-02 2.50e+03 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 112 2.54 - 3.13: 10724 3.13 - 3.72: 19550 3.72 - 4.31: 27431 4.31 - 4.90: 48659 Nonbonded interactions: 106476 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 1.951 3.040 nonbonded pdb=" O GLU F 258 " pdb=" OG1 THR F 317 " model vdw 2.026 3.040 nonbonded pdb=" OG SER G 99 " pdb=" OG SER G 104 " model vdw 2.084 3.040 nonbonded pdb=" O LEU E 212 " pdb=" NH1 ARG E 257 " model vdw 2.104 3.120 nonbonded pdb=" OE1 GLN G 38 " pdb=" OH TYR G 94 " model vdw 2.109 3.040 ... (remaining 106471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' 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 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: 11.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.750 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 : 0.024 1.660 14477 Z= 1.128 Angle : 1.035 80.499 19649 Z= 0.709 Chirality : 0.043 0.194 2139 Planarity : 0.009 0.273 2531 Dihedral : 14.690 89.525 5283 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.12 % Favored : 92.77 % Rotamer: Outliers : 0.38 % Allowed : 11.91 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.41 (0.20), residues: 1798 helix: -1.44 (0.53), residues: 86 sheet: -0.54 (0.21), residues: 595 loop : -1.11 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 35 HIS 0.005 0.001 HIS F 113 PHE 0.013 0.001 PHE F 133 TYR 0.013 0.001 TYR D 95 ARG 0.004 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 159 average time/residue: 0.2926 time to fit residues: 65.7509 Evaluate side-chains 142 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain F residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 203 HIS C 167 GLN C 199 HIS C 211 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 HIS F 254 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 14477 Z= 0.325 Angle : 0.739 9.577 19649 Z= 0.386 Chirality : 0.048 0.210 2139 Planarity : 0.006 0.087 2531 Dihedral : 6.354 59.195 2042 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.60 % Favored : 93.29 % Rotamer: Outliers : 2.82 % Allowed : 13.44 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.41 (0.19), residues: 1804 helix: -1.39 (0.52), residues: 85 sheet: -0.33 (0.21), residues: 621 loop : -1.27 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 35 HIS 0.009 0.001 HIS F 113 PHE 0.018 0.002 PHE E 323 TYR 0.018 0.002 TYR A 50 ARG 0.008 0.001 ARG F 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6551 (tp) REVERT: E 34 TYR cc_start: 0.5729 (OUTLIER) cc_final: 0.5372 (m-80) REVERT: F 233 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7356 (p) REVERT: F 323 PHE cc_start: 0.6646 (OUTLIER) cc_final: 0.5334 (m-80) outliers start: 44 outliers final: 27 residues processed: 181 average time/residue: 0.2593 time to fit residues: 68.8168 Evaluate side-chains 165 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 344 ASN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 323 PHE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 163 optimal weight: 20.0000 chunk 176 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14477 Z= 0.252 Angle : 0.658 11.040 19649 Z= 0.342 Chirality : 0.045 0.214 2139 Planarity : 0.005 0.070 2531 Dihedral : 6.121 59.206 2040 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 3.39 % Allowed : 14.53 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1804 helix: -1.04 (0.53), residues: 85 sheet: -0.21 (0.21), residues: 629 loop : -1.22 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 35 HIS 0.008 0.001 HIS F 113 PHE 0.017 0.002 PHE E 323 TYR 0.014 0.001 TYR A 50 ARG 0.006 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.5109 (tm-30) REVERT: D 76 LYS cc_start: 0.5304 (tppt) cc_final: 0.4881 (mmtp) REVERT: E 34 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.5382 (m-80) REVERT: E 202 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6819 (mt) outliers start: 53 outliers final: 32 residues processed: 186 average time/residue: 0.2714 time to fit residues: 73.8150 Evaluate side-chains 163 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 155 optimal weight: 0.0030 chunk 46 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14477 Z= 0.331 Angle : 0.737 10.526 19649 Z= 0.382 Chirality : 0.047 0.198 2139 Planarity : 0.006 0.091 2531 Dihedral : 6.400 59.700 2038 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.41 % Rotamer: Outliers : 4.74 % Allowed : 15.88 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.45 (0.19), residues: 1804 helix: -1.38 (0.52), residues: 79 sheet: -0.18 (0.21), residues: 614 loop : -1.44 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 210 HIS 0.008 0.002 HIS E 35 PHE 0.018 0.002 PHE E 323 TYR 0.019 0.002 TYR A 50 ARG 0.012 0.001 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 135 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.5172 (tm-30) REVERT: B 195 GLN cc_start: 0.3984 (OUTLIER) cc_final: 0.3743 (mp10) REVERT: D 67 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7059 (mtm110) REVERT: D 76 LYS cc_start: 0.5393 (tppt) cc_final: 0.4973 (mmtp) REVERT: E 34 TYR cc_start: 0.5900 (OUTLIER) cc_final: 0.5573 (m-80) REVERT: E 202 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6838 (mt) REVERT: F 131 ASN cc_start: 0.7268 (OUTLIER) cc_final: 0.6990 (p0) REVERT: F 233 THR cc_start: 0.7577 (OUTLIER) cc_final: 0.7355 (p) outliers start: 74 outliers final: 48 residues processed: 201 average time/residue: 0.2554 time to fit residues: 76.1332 Evaluate side-chains 177 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 122 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.0000 chunk 156 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14477 Z= 0.262 Angle : 0.665 10.175 19649 Z= 0.344 Chirality : 0.045 0.173 2139 Planarity : 0.006 0.088 2531 Dihedral : 6.160 59.191 2038 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.04 % Favored : 93.85 % Rotamer: Outliers : 4.29 % Allowed : 16.71 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1804 helix: -1.13 (0.54), residues: 79 sheet: -0.15 (0.22), residues: 619 loop : -1.39 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 115 HIS 0.008 0.001 HIS F 113 PHE 0.016 0.002 PHE A 63 TYR 0.015 0.001 TYR A 50 ARG 0.008 0.000 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 130 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.5169 (tm-30) REVERT: C 18 ASP cc_start: 0.6885 (t0) cc_final: 0.6678 (t0) REVERT: D 67 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7049 (mtm110) REVERT: D 76 LYS cc_start: 0.5379 (tppt) cc_final: 0.4977 (mmtp) REVERT: E 34 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5483 (m-80) REVERT: E 202 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6773 (mt) REVERT: F 233 THR cc_start: 0.7575 (OUTLIER) cc_final: 0.7353 (p) outliers start: 67 outliers final: 50 residues processed: 189 average time/residue: 0.2746 time to fit residues: 75.3722 Evaluate side-chains 179 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 82 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN F 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14477 Z= 0.168 Angle : 0.574 9.723 19649 Z= 0.298 Chirality : 0.043 0.156 2139 Planarity : 0.005 0.089 2531 Dihedral : 5.668 59.028 2038 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 3.01 % Allowed : 18.25 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -1.05 (0.20), residues: 1804 helix: -0.55 (0.54), residues: 87 sheet: 0.06 (0.22), residues: 621 loop : -1.20 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 115 HIS 0.006 0.001 HIS F 113 PHE 0.015 0.001 PHE A 140 TYR 0.013 0.001 TYR D 95 ARG 0.006 0.000 ARG F 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.5167 (tm-30) REVERT: D 76 LYS cc_start: 0.5403 (tppt) cc_final: 0.4972 (mmtp) REVERT: D 211 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: E 34 TYR cc_start: 0.5669 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: E 202 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6756 (mt) REVERT: F 118 TRP cc_start: 0.4457 (OUTLIER) cc_final: 0.4015 (m-90) outliers start: 47 outliers final: 26 residues processed: 173 average time/residue: 0.2831 time to fit residues: 70.7425 Evaluate side-chains 151 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.134 14477 Z= 0.667 Angle : 1.015 13.111 19649 Z= 0.529 Chirality : 0.058 0.258 2139 Planarity : 0.009 0.129 2531 Dihedral : 7.398 58.799 2038 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.20 % Favored : 89.63 % Rotamer: Outliers : 6.02 % Allowed : 16.77 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.19), residues: 1804 helix: -2.24 (0.47), residues: 79 sheet: -0.54 (0.22), residues: 601 loop : -1.94 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP F 330 HIS 0.017 0.003 HIS E 35 PHE 0.035 0.004 PHE E 323 TYR 0.031 0.003 TYR B 94 ARG 0.013 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 126 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5181 (tm-30) REVERT: D 67 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7372 (mtm110) REVERT: E 34 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5868 (m-80) REVERT: E 52 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: E 86 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7438 (tp) REVERT: E 331 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: F 233 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7430 (p) REVERT: F 324 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.3413 (mmm160) REVERT: H 102 PHE cc_start: 0.4325 (OUTLIER) cc_final: 0.3965 (m-80) outliers start: 94 outliers final: 64 residues processed: 207 average time/residue: 0.2619 time to fit residues: 79.1301 Evaluate side-chains 187 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 114 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 34 TYR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 85 GLN Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 233 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 102 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 0.0670 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 85 optimal weight: 0.0020 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14477 Z= 0.177 Angle : 0.620 9.541 19649 Z= 0.324 Chirality : 0.044 0.201 2139 Planarity : 0.005 0.073 2531 Dihedral : 5.972 57.764 2037 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.01 % Rotamer: Outliers : 2.62 % Allowed : 20.61 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.06 % 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: -1.42 (0.19), residues: 1804 helix: -1.05 (0.52), residues: 81 sheet: -0.10 (0.22), residues: 599 loop : -1.47 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 330 HIS 0.008 0.001 HIS F 113 PHE 0.014 0.001 PHE A 140 TYR 0.015 0.001 TYR D 95 ARG 0.007 0.000 ARG E 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.5136 (tm-30) REVERT: E 34 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.5563 (m-80) REVERT: E 202 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6665 (mt) REVERT: F 324 ARG cc_start: 0.5628 (OUTLIER) cc_final: 0.3423 (mmm160) outliers start: 41 outliers final: 30 residues processed: 148 average time/residue: 0.2780 time to fit residues: 60.3571 Evaluate side-chains 147 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 ARG Chi-restraints excluded: chain H residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 152 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14477 Z= 0.317 Angle : 0.718 10.416 19649 Z= 0.372 Chirality : 0.046 0.178 2139 Planarity : 0.006 0.085 2531 Dihedral : 6.239 58.573 2037 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 3.20 % Allowed : 20.10 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -1.54 (0.19), residues: 1804 helix: -1.10 (0.54), residues: 79 sheet: -0.18 (0.22), residues: 604 loop : -1.56 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 150 HIS 0.008 0.002 HIS F 113 PHE 0.022 0.002 PHE E 323 TYR 0.016 0.002 TYR D 95 ARG 0.008 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 121 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.5244 (tm-30) REVERT: D 76 LYS cc_start: 0.5335 (tppt) cc_final: 0.5006 (mmtp) REVERT: E 202 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6818 (mt) REVERT: E 331 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6745 (m-80) REVERT: F 324 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.3386 (mmm160) outliers start: 50 outliers final: 36 residues processed: 164 average time/residue: 0.2816 time to fit residues: 67.1169 Evaluate side-chains 157 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 117 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 118 optimal weight: 0.4980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 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 90 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN H 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14477 Z= 0.236 Angle : 0.654 10.440 19649 Z= 0.338 Chirality : 0.044 0.190 2139 Planarity : 0.005 0.068 2531 Dihedral : 5.906 58.256 2035 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.93 % Favored : 93.96 % Rotamer: Outliers : 2.69 % Allowed : 20.93 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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: -1.39 (0.20), residues: 1804 helix: -0.85 (0.56), residues: 79 sheet: -0.12 (0.21), residues: 626 loop : -1.47 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 115 HIS 0.007 0.001 HIS F 113 PHE 0.016 0.002 PHE A 140 TYR 0.015 0.001 TYR E 34 ARG 0.006 0.000 ARG B 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3608 Ramachandran restraints generated. 1804 Oldfield, 0 Emsley, 1804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5251 (tm-30) REVERT: B 47 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: D 76 LYS cc_start: 0.5285 (tppt) cc_final: 0.4923 (mmtp) REVERT: E 202 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6770 (mt) REVERT: E 331 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: F 324 ARG cc_start: 0.5661 (OUTLIER) cc_final: 0.3446 (mmm160) outliers start: 42 outliers final: 33 residues processed: 150 average time/residue: 0.2711 time to fit residues: 59.0179 Evaluate side-chains 151 residues out of total 1562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 324 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 0.0470 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 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 = 0.4660 r_free = 0.4660 target = 0.218414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.178745 restraints weight = 17688.224| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.59 r_work: 0.4071 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14477 Z= 0.281 Angle : 0.693 10.599 19649 Z= 0.356 Chirality : 0.045 0.164 2139 Planarity : 0.006 0.070 2531 Dihedral : 6.048 58.722 2035 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.87 % Favored : 92.02 % Rotamer: Outliers : 3.01 % Allowed : 20.55 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 1.14 % 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 (0.19), residues: 1804 helix: -0.98 (0.55), residues: 79 sheet: -0.17 (0.21), residues: 620 loop : -1.52 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 115 HIS 0.007 0.001 HIS F 113 PHE 0.018 0.002 PHE E 323 TYR 0.015 0.002 TYR A 50 ARG 0.008 0.001 ARG B 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3820.42 seconds wall clock time: 70 minutes 3.53 seconds (4203.53 seconds total)