Starting phenix.real_space_refine on Sat Mar 16 22:41:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7a_41089/03_2024/8t7a_41089_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7a_41089/03_2024/8t7a_41089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7a_41089/03_2024/8t7a_41089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7a_41089/03_2024/8t7a_41089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7a_41089/03_2024/8t7a_41089_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7a_41089/03_2024/8t7a_41089_neut.pdb" } resolution = 2.8 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= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9990 2.51 5 N 2616 2.21 5 O 3129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 49": "NH1" <-> "NH2" Residue "a ARG 229": "NH1" <-> "NH2" Residue "a ARG 235": "NH1" <-> "NH2" Residue "a ARG 282": "NH1" <-> "NH2" Residue "a ARG 336": "NH1" <-> "NH2" Residue "a ARG 339": "NH1" <-> "NH2" Residue "a ARG 364": "NH1" <-> "NH2" Residue "a ARG 429": "NH1" <-> "NH2" Residue "a PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "b ARG 229": "NH1" <-> "NH2" Residue "b ARG 235": "NH1" <-> "NH2" Residue "b ARG 282": "NH1" <-> "NH2" Residue "b ARG 336": "NH1" <-> "NH2" Residue "b ARG 339": "NH1" <-> "NH2" Residue "b ARG 364": "NH1" <-> "NH2" Residue "b ARG 429": "NH1" <-> "NH2" Residue "b PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "c ARG 229": "NH1" <-> "NH2" Residue "c ARG 235": "NH1" <-> "NH2" Residue "c ARG 282": "NH1" <-> "NH2" Residue "c ARG 336": "NH1" <-> "NH2" Residue "c ARG 339": "NH1" <-> "NH2" Residue "c ARG 364": "NH1" <-> "NH2" Residue "c ARG 429": "NH1" <-> "NH2" Residue "c PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ASP 86": "OD1" <-> "OD2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 17": "OE1" <-> "OE2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 27": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15819 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "a" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "B" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "b" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "c" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2847 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "D" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "E" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "F" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "G" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 963 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "I" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "a" 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: "b" 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: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.64, per 1000 atoms: 0.55 Number of scatterers: 15819 At special positions: 0 Unit cell: (125.96, 124.08, 133.48, 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 84 16.00 O 3129 8.00 N 2616 7.00 C 9990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS a 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS a 212 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 343 " distance=2.02 Simple disulfide: pdb=" SG CYS a 322 " - pdb=" SG CYS a 333 " distance=2.03 Simple disulfide: pdb=" SG CYS a 358 " - pdb=" SG CYS a 367 " distance=2.03 Simple disulfide: pdb=" SG CYS a 382 " - pdb=" SG CYS a 393 " distance=2.03 Simple disulfide: pdb=" SG CYS a 416 " - pdb=" SG CYS a 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS b 439 " distance=2.02 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS b 212 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 343 " distance=2.05 Simple disulfide: pdb=" SG CYS b 322 " - pdb=" SG CYS b 333 " distance=2.03 Simple disulfide: pdb=" SG CYS b 358 " - pdb=" SG CYS b 367 " distance=2.03 Simple disulfide: pdb=" SG CYS b 382 " - pdb=" SG CYS b 393 " distance=2.03 Simple disulfide: pdb=" SG CYS b 416 " - pdb=" SG CYS b 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS c 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS c 212 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 343 " distance=2.05 Simple disulfide: pdb=" SG CYS c 322 " - pdb=" SG CYS c 333 " distance=2.02 Simple disulfide: pdb=" SG CYS c 358 " - pdb=" SG CYS c 367 " distance=2.03 Simple disulfide: pdb=" SG CYS c 382 " - pdb=" SG CYS c 393 " distance=2.03 Simple disulfide: pdb=" SG CYS c 416 " - pdb=" SG CYS c 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG a 601 " - " ASN a 500 " " NAG b 601 " - " ASN b 500 " " NAG c 601 " - " ASN c 500 " Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.9 seconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 34 sheets defined 22.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 73 through 98 removed outlier: 3.518A pdb=" N LYS A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 138 through 142 Processing helix chain 'a' and resid 148 through 158 Processing helix chain 'a' and resid 162 through 171 Processing helix chain 'a' and resid 195 through 203 removed outlier: 3.726A pdb=" N LEU a 203 " --> pdb=" O ILE a 199 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 241 removed outlier: 4.485A pdb=" N VAL a 220 " --> pdb=" O ASN a 216 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG a 229 " --> pdb=" O GLN a 225 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU a 230 " --> pdb=" O LYS a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 253 through 264 Processing helix chain 'a' and resid 267 through 276 Processing helix chain 'a' and resid 277 through 284 Processing helix chain 'a' and resid 370 through 372 No H-bonds generated for 'chain 'a' and resid 370 through 372' Processing helix chain 'a' and resid 376 through 379 Processing helix chain 'a' and resid 380 through 385 removed outlier: 3.948A pdb=" N VAL a 384 " --> pdb=" O ASN a 380 " (cutoff:3.500A) Processing helix chain 'a' and resid 473 through 477 Processing helix chain 'a' and resid 492 through 503 Processing helix chain 'B' and resid 73 through 98 removed outlier: 3.518A pdb=" N LYS B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 138 through 142 Processing helix chain 'b' and resid 148 through 158 Processing helix chain 'b' and resid 162 through 171 Processing helix chain 'b' and resid 195 through 203 removed outlier: 3.726A pdb=" N LEU b 203 " --> pdb=" O ILE b 199 " (cutoff:3.500A) Processing helix chain 'b' and resid 216 through 241 removed outlier: 4.487A pdb=" N VAL b 220 " --> pdb=" O ASN b 216 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG b 229 " --> pdb=" O GLN b 225 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU b 230 " --> pdb=" O LYS b 226 " (cutoff:3.500A) Processing helix chain 'b' and resid 253 through 264 Processing helix chain 'b' and resid 267 through 276 Processing helix chain 'b' and resid 277 through 284 Processing helix chain 'b' and resid 370 through 372 No H-bonds generated for 'chain 'b' and resid 370 through 372' Processing helix chain 'b' and resid 376 through 379 Processing helix chain 'b' and resid 380 through 385 removed outlier: 3.948A pdb=" N VAL b 384 " --> pdb=" O ASN b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 473 through 478 Processing helix chain 'b' and resid 492 through 503 Processing helix chain 'C' and resid 73 through 98 removed outlier: 3.518A pdb=" N LYS C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 137 through 142 removed outlier: 4.482A pdb=" N PHE c 140 " --> pdb=" O PHE c 137 " (cutoff:3.500A) Processing helix chain 'c' and resid 148 through 158 Processing helix chain 'c' and resid 162 through 171 Processing helix chain 'c' and resid 195 through 203 removed outlier: 3.727A pdb=" N LEU c 203 " --> pdb=" O ILE c 199 " (cutoff:3.500A) Processing helix chain 'c' and resid 216 through 241 removed outlier: 4.485A pdb=" N VAL c 220 " --> pdb=" O ASN c 216 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG c 229 " --> pdb=" O GLN c 225 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU c 230 " --> pdb=" O LYS c 226 " (cutoff:3.500A) Processing helix chain 'c' and resid 253 through 264 Processing helix chain 'c' and resid 267 through 276 Processing helix chain 'c' and resid 277 through 284 Processing helix chain 'c' and resid 370 through 372 No H-bonds generated for 'chain 'c' and resid 370 through 372' Processing helix chain 'c' and resid 376 through 379 Processing helix chain 'c' and resid 380 through 385 removed outlier: 3.947A pdb=" N VAL c 384 " --> pdb=" O ASN c 380 " (cutoff:3.500A) Processing helix chain 'c' and resid 473 through 478 Processing helix chain 'c' and resid 492 through 503 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'a' and resid 359 through 361 removed outlier: 7.014A pdb=" N SER A 38 " --> pdb=" O THR a 318 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR a 318 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A 40 " --> pdb=" O LEU a 316 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU a 316 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 42 " --> pdb=" O TRP a 314 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP a 314 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR A 44 " --> pdb=" O PRO a 312 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER A 46 " --> pdb=" O ASP a 310 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL a 308 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 359 through 361 Processing sheet with id=AA3, first strand: chain 'a' and resid 176 through 180 removed outlier: 10.895A pdb=" N SER a 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR A 54 " --> pdb=" O SER a 186 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU a 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU A 60 " --> pdb=" O VAL a 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP a 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL a 296 " --> pdb=" O ILE a 292 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE a 292 " --> pdb=" O VAL a 296 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA a 298 " --> pdb=" O SER a 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 321 through 322 removed outlier: 7.299A pdb=" N ILE a 395 " --> pdb=" O ASP a 489 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP a 489 " --> pdb=" O ILE a 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'a' and resid 430 through 435 removed outlier: 6.599A pdb=" N ALA a 424 " --> pdb=" O ILE a 432 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N THR a 434 " --> pdb=" O CYS a 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS a 422 " --> pdb=" O THR a 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 359 through 361 removed outlier: 7.071A pdb=" N SER B 38 " --> pdb=" O THR b 318 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR b 318 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 40 " --> pdb=" O LEU b 316 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU b 316 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS B 42 " --> pdb=" O TRP b 314 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP b 314 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 44 " --> pdb=" O PRO b 312 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER B 46 " --> pdb=" O ASP b 310 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL b 308 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 359 through 361 Processing sheet with id=AA9, first strand: chain 'b' and resid 176 through 180 removed outlier: 10.895A pdb=" N SER b 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR B 54 " --> pdb=" O SER b 186 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU b 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLU B 60 " --> pdb=" O VAL b 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP b 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL b 296 " --> pdb=" O ILE b 292 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE b 292 " --> pdb=" O VAL b 296 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA b 298 " --> pdb=" O SER b 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 321 through 322 removed outlier: 7.272A pdb=" N ILE b 395 " --> pdb=" O ASP b 489 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP b 489 " --> pdb=" O ILE b 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'b' and resid 430 through 435 removed outlier: 6.599A pdb=" N ALA b 424 " --> pdb=" O ILE b 432 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR b 434 " --> pdb=" O CYS b 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS b 422 " --> pdb=" O THR b 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 359 through 361 removed outlier: 6.991A pdb=" N SER C 38 " --> pdb=" O THR c 318 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR c 318 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL C 40 " --> pdb=" O LEU c 316 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU c 316 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS C 42 " --> pdb=" O TRP c 314 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP c 314 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR C 44 " --> pdb=" O PRO c 312 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER C 46 " --> pdb=" O ASP c 310 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL c 308 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 359 through 361 Processing sheet with id=AB6, first strand: chain 'c' and resid 176 through 180 removed outlier: 10.895A pdb=" N SER c 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR C 54 " --> pdb=" O SER c 186 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU c 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU C 60 " --> pdb=" O VAL c 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP c 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL c 296 " --> pdb=" O ILE c 292 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE c 292 " --> pdb=" O VAL c 296 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA c 298 " --> pdb=" O SER c 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 321 through 322 removed outlier: 7.289A pdb=" N ILE c 395 " --> pdb=" O ASP c 489 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP c 489 " --> pdb=" O ILE c 395 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'c' and resid 430 through 435 removed outlier: 6.600A pdb=" N ALA c 424 " --> pdb=" O ILE c 432 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR c 434 " --> pdb=" O CYS c 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS c 422 " --> pdb=" O THR c 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.521A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 33 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR D 32 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER D 52 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.607A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.523A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 27C through 27D Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.522A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR F 32 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N SER F 52 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.606A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.523A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 27C through 27D Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.521A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR H 32 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N SER H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.607A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.523A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 27C through 27D 766 hydrogen bonds defined for protein. 1953 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: 5.66 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2630 1.30 - 1.43: 4003 1.43 - 1.56: 9345 1.56 - 1.69: 3 1.69 - 1.82: 114 Bond restraints: 16095 Sorted by residual: bond pdb=" C VAL a 406 " pdb=" O VAL a 406 " ideal model delta sigma weight residual 1.237 1.166 0.072 1.08e-02 8.57e+03 4.42e+01 bond pdb=" C ILE c 332 " pdb=" O ILE c 332 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.02e-02 9.61e+03 3.91e+01 bond pdb=" C SER a 415 " pdb=" O SER a 415 " ideal model delta sigma weight residual 1.235 1.168 0.068 1.19e-02 7.06e+03 3.23e+01 bond pdb=" N TYR c 417 " pdb=" CA TYR c 417 " ideal model delta sigma weight residual 1.455 1.384 0.070 1.26e-02 6.30e+03 3.10e+01 bond pdb=" C THR a 335 " pdb=" O THR a 335 " ideal model delta sigma weight residual 1.234 1.165 0.069 1.26e-02 6.30e+03 3.04e+01 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.50: 256 105.50 - 112.64: 8664 112.64 - 119.78: 5125 119.78 - 126.92: 7667 126.92 - 134.06: 140 Bond angle restraints: 21852 Sorted by residual: angle pdb=" N CYS c 333 " pdb=" CA CYS c 333 " pdb=" C CYS c 333 " ideal model delta sigma weight residual 109.81 121.51 -11.70 1.53e+00 4.27e-01 5.85e+01 angle pdb=" N CYS b 333 " pdb=" CA CYS b 333 " pdb=" C CYS b 333 " ideal model delta sigma weight residual 109.52 120.27 -10.75 1.55e+00 4.16e-01 4.81e+01 angle pdb=" N SER c 275 " pdb=" CA SER c 275 " pdb=" C SER c 275 " ideal model delta sigma weight residual 111.71 104.48 7.23 1.15e+00 7.56e-01 3.95e+01 angle pdb=" N SER a 275 " pdb=" CA SER a 275 " pdb=" C SER a 275 " ideal model delta sigma weight residual 111.71 104.51 7.20 1.15e+00 7.56e-01 3.92e+01 angle pdb=" N SER b 275 " pdb=" CA SER b 275 " pdb=" C SER b 275 " ideal model delta sigma weight residual 111.71 104.52 7.19 1.15e+00 7.56e-01 3.91e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 8942 17.11 - 34.21: 608 34.21 - 51.32: 183 51.32 - 68.43: 49 68.43 - 85.54: 13 Dihedral angle restraints: 9795 sinusoidal: 3858 harmonic: 5937 Sorted by residual: dihedral pdb=" CB CYS b 358 " pdb=" SG CYS b 358 " pdb=" SG CYS b 367 " pdb=" CB CYS b 367 " ideal model delta sinusoidal sigma weight residual 93.00 128.74 -35.74 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS c 358 " pdb=" SG CYS c 358 " pdb=" SG CYS c 367 " pdb=" CB CYS c 367 " ideal model delta sinusoidal sigma weight residual 93.00 128.74 -35.74 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS a 358 " pdb=" SG CYS a 358 " pdb=" SG CYS a 367 " pdb=" CB CYS a 367 " ideal model delta sinusoidal sigma weight residual 93.00 128.70 -35.70 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 9792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2485 0.109 - 0.217: 83 0.217 - 0.326: 3 0.326 - 0.434: 0 0.434 - 0.543: 3 Chirality restraints: 2574 Sorted by residual: chirality pdb=" CG LEU c 158 " pdb=" CB LEU c 158 " pdb=" CD1 LEU c 158 " pdb=" CD2 LEU c 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" CG LEU b 158 " pdb=" CB LEU b 158 " pdb=" CD1 LEU b 158 " pdb=" CD2 LEU b 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CG LEU a 158 " pdb=" CB LEU a 158 " pdb=" CD1 LEU a 158 " pdb=" CD2 LEU a 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 2571 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 81 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" CD GLN A 81 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN A 81 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN A 81 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 81 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" CD GLN C 81 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN C 81 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN C 81 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 81 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" CD GLN B 81 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN B 81 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN B 81 " -0.019 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1480 2.75 - 3.29: 15149 3.29 - 3.82: 26191 3.82 - 4.36: 32319 4.36 - 4.90: 56521 Nonbonded interactions: 131660 Sorted by model distance: nonbonded pdb=" OG SER b 290 " pdb=" O ALA b 298 " model vdw 2.212 2.440 nonbonded pdb=" OG SER a 290 " pdb=" O ALA a 298 " model vdw 2.213 2.440 nonbonded pdb=" OG SER c 290 " pdb=" O ALA c 298 " model vdw 2.213 2.440 nonbonded pdb=" O SER D 7 " pdb=" OG1 THR D 107 " model vdw 2.263 2.440 nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 107 " model vdw 2.263 2.440 ... (remaining 131655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 3.430 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: 0.010 Extract box with map and model: 12.780 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.860 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16095 Z= 0.351 Angle : 0.714 11.698 21852 Z= 0.416 Chirality : 0.050 0.543 2574 Planarity : 0.006 0.081 2757 Dihedral : 13.491 85.537 5904 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.66 % Allowed : 11.44 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.46 (0.19), residues: 2016 helix: 0.86 (0.27), residues: 366 sheet: 0.52 (0.20), residues: 684 loop : 0.06 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 52 HIS 0.005 0.002 HIS b 159 PHE 0.030 0.002 PHE b 140 TYR 0.018 0.002 TYR c 417 ARG 0.015 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 1.797 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7601 (mttp) REVERT: A 88 ASN cc_start: 0.8268 (m-40) cc_final: 0.7977 (m-40) REVERT: B 87 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7537 (mttp) REVERT: b 429 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7709 (mtp180) REVERT: b 465 LYS cc_start: 0.8173 (tmtt) cc_final: 0.7518 (tttm) REVERT: C 87 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7534 (mttp) REVERT: C 88 ASN cc_start: 0.8168 (m-40) cc_final: 0.7954 (m-40) REVERT: c 202 GLN cc_start: 0.7934 (mt0) cc_final: 0.7625 (mt0) REVERT: c 465 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7566 (tttm) REVERT: H 3 GLN cc_start: 0.8536 (pt0) cc_final: 0.8302 (pt0) REVERT: I 89 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8295 (tt0) outliers start: 12 outliers final: 6 residues processed: 226 average time/residue: 1.2649 time to fit residues: 317.6252 Evaluate side-chains 171 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 404 SER Chi-restraints excluded: chain b residue 161 GLU Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain I residue 89 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 277 ASN b 317 HIS C 34 GLN D 58 ASN G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16095 Z= 0.253 Angle : 0.521 8.347 21852 Z= 0.277 Chirality : 0.044 0.148 2574 Planarity : 0.004 0.054 2757 Dihedral : 5.414 52.933 2260 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.59 % Allowed : 12.38 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.96 (0.19), residues: 2016 helix: 2.09 (0.27), residues: 372 sheet: 0.73 (0.20), residues: 675 loop : 0.08 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 36 HIS 0.005 0.001 HIS a 317 PHE 0.009 0.001 PHE a 483 TYR 0.026 0.002 TYR H 100E ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7700 (ttmt) REVERT: a 324 THR cc_start: 0.8525 (p) cc_final: 0.8174 (p) REVERT: B 87 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7627 (ttmt) REVERT: b 429 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7620 (mtp180) REVERT: b 465 LYS cc_start: 0.8185 (tmtt) cc_final: 0.7474 (tttm) REVERT: C 31 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 77 LYS cc_start: 0.8123 (mttm) cc_final: 0.7623 (mmtt) REVERT: C 87 LYS cc_start: 0.8091 (ttpp) cc_final: 0.7824 (ttpt) REVERT: c 202 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: c 297 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8035 (tp) REVERT: c 324 THR cc_start: 0.8251 (p) cc_final: 0.8028 (p) REVERT: c 465 LYS cc_start: 0.8302 (tmtt) cc_final: 0.7575 (tttm) REVERT: c 498 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7791 (mtpt) outliers start: 65 outliers final: 24 residues processed: 231 average time/residue: 1.2241 time to fit residues: 313.6441 Evaluate side-chains 197 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 384 VAL Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 34 GLN C 98 GLN D 58 ASN I 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16095 Z= 0.246 Angle : 0.509 7.952 21852 Z= 0.268 Chirality : 0.044 0.150 2574 Planarity : 0.004 0.044 2757 Dihedral : 5.176 53.886 2250 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.43 % Allowed : 13.65 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.00 (0.19), residues: 2016 helix: 2.31 (0.27), residues: 372 sheet: 0.73 (0.20), residues: 675 loop : 0.03 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 36 HIS 0.005 0.001 HIS a 317 PHE 0.010 0.001 PHE b 137 TYR 0.023 0.002 TYR H 100E ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 173 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7723 (ttmt) REVERT: a 324 THR cc_start: 0.8496 (p) cc_final: 0.8137 (p) REVERT: B 87 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7597 (ttmt) REVERT: b 165 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7720 (m110) REVERT: b 429 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7624 (mtp180) REVERT: b 465 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7485 (tttm) REVERT: C 31 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: C 77 LYS cc_start: 0.8090 (mttm) cc_final: 0.7610 (mmtt) REVERT: C 87 LYS cc_start: 0.8164 (ttpp) cc_final: 0.7922 (ttpt) REVERT: c 202 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: c 324 THR cc_start: 0.8081 (p) cc_final: 0.7857 (p) REVERT: c 465 LYS cc_start: 0.8314 (tmtt) cc_final: 0.7583 (tttm) REVERT: c 498 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7667 (mtpt) REVERT: D 46 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: E 89 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: F 46 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: H 46 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6495 (tm-30) outliers start: 62 outliers final: 34 residues processed: 215 average time/residue: 1.2350 time to fit residues: 294.5385 Evaluate side-chains 212 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 164 VAL Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 34 GLN C 98 GLN D 58 ASN I 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16095 Z= 0.202 Angle : 0.480 7.598 21852 Z= 0.253 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.038 2757 Dihedral : 5.066 53.683 2250 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.81 % Allowed : 14.43 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.03 (0.19), residues: 2016 helix: 2.49 (0.27), residues: 372 sheet: 0.75 (0.20), residues: 675 loop : -0.02 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.005 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.016 0.001 TYR H 100E ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 173 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8069 (mttm) cc_final: 0.7450 (mmtt) REVERT: A 87 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7702 (ttmt) REVERT: a 202 GLN cc_start: 0.8049 (mt0) cc_final: 0.7782 (mt0) REVERT: B 87 LYS cc_start: 0.8014 (ttpp) cc_final: 0.7618 (ttmt) REVERT: b 165 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7677 (m110) REVERT: b 429 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7624 (mtp180) REVERT: b 465 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7506 (tttm) REVERT: b 498 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7514 (mtpt) REVERT: C 31 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: C 77 LYS cc_start: 0.8078 (mttm) cc_final: 0.7563 (mmtt) REVERT: C 87 LYS cc_start: 0.8161 (ttpp) cc_final: 0.7914 (ttpt) REVERT: c 202 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: c 297 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8084 (tp) REVERT: c 465 LYS cc_start: 0.8282 (tmtt) cc_final: 0.7567 (tttm) REVERT: c 498 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7671 (mtpt) REVERT: D 46 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: D 105 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7982 (pt0) REVERT: E 89 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: F 46 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: H 46 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6497 (tm-30) outliers start: 69 outliers final: 44 residues processed: 223 average time/residue: 1.2254 time to fit residues: 302.9440 Evaluate side-chains 222 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 165 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 34 GLN C 98 GLN I 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16095 Z= 0.191 Angle : 0.474 8.336 21852 Z= 0.249 Chirality : 0.043 0.148 2574 Planarity : 0.003 0.040 2757 Dihedral : 5.027 53.990 2250 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.26 % Allowed : 14.48 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 1.03 (0.19), residues: 2016 helix: 2.58 (0.27), residues: 372 sheet: 0.73 (0.20), residues: 675 loop : -0.04 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.015 0.001 TYR c 457 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 174 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8075 (mttm) cc_final: 0.7455 (mmtt) REVERT: A 87 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7604 (ttmt) REVERT: a 202 GLN cc_start: 0.8019 (mt0) cc_final: 0.7746 (mt0) REVERT: B 87 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7613 (ttmt) REVERT: b 165 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7717 (m110) REVERT: b 429 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7560 (mtm110) REVERT: b 465 LYS cc_start: 0.8168 (tmtt) cc_final: 0.7479 (tttm) REVERT: b 498 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7484 (mtpt) REVERT: C 31 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: C 77 LYS cc_start: 0.8099 (mttm) cc_final: 0.7568 (mmtt) REVERT: C 87 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7911 (ttpt) REVERT: c 202 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: c 297 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8072 (tp) REVERT: c 465 LYS cc_start: 0.8268 (tmtt) cc_final: 0.7557 (tttm) REVERT: c 498 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7735 (mtpt) REVERT: D 46 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6910 (tt0) REVERT: D 105 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: E 89 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: F 46 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: H 46 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6488 (tm-30) outliers start: 77 outliers final: 52 residues processed: 228 average time/residue: 1.1756 time to fit residues: 298.2262 Evaluate side-chains 231 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 168 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 212 CYS Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 98 GLN D 58 ASN F 39 GLN G 38 GLN I 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16095 Z= 0.260 Angle : 0.510 9.106 21852 Z= 0.268 Chirality : 0.044 0.146 2574 Planarity : 0.004 0.041 2757 Dihedral : 5.191 54.200 2250 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.20 % Allowed : 15.20 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.90 (0.19), residues: 2016 helix: 2.47 (0.27), residues: 372 sheet: 0.63 (0.20), residues: 675 loop : -0.11 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 36 HIS 0.005 0.001 HIS a 317 PHE 0.010 0.001 PHE b 137 TYR 0.018 0.002 TYR c 457 ARG 0.003 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 174 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7713 (ttmt) REVERT: a 165 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: a 202 GLN cc_start: 0.8032 (mt0) cc_final: 0.7782 (mt0) REVERT: B 87 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7575 (ttmt) REVERT: b 165 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7707 (m110) REVERT: b 180 SER cc_start: 0.8881 (p) cc_final: 0.8557 (p) REVERT: b 429 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7547 (mtm110) REVERT: b 465 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7502 (tttm) REVERT: b 498 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7494 (mtpt) REVERT: C 31 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: C 87 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7954 (ttpt) REVERT: c 202 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: c 297 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8107 (tp) REVERT: c 465 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7551 (tttm) REVERT: c 498 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7730 (mtpt) REVERT: D 46 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: D 105 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: E 89 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: F 46 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: F 69 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: H 46 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6486 (tm-30) outliers start: 76 outliers final: 55 residues processed: 230 average time/residue: 1.2561 time to fit residues: 320.6987 Evaluate side-chains 235 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 167 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 212 CYS Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 193 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN ** b 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 39 GLN G 38 GLN I 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16095 Z= 0.230 Angle : 0.493 10.098 21852 Z= 0.259 Chirality : 0.043 0.148 2574 Planarity : 0.004 0.045 2757 Dihedral : 5.131 54.093 2250 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.15 % Allowed : 15.75 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.92 (0.19), residues: 2016 helix: 2.56 (0.27), residues: 372 sheet: 0.64 (0.20), residues: 675 loop : -0.13 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.005 0.001 HIS a 317 PHE 0.010 0.001 PHE b 137 TYR 0.016 0.002 TYR c 457 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 171 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7707 (ttmt) REVERT: a 165 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7650 (m-40) REVERT: a 202 GLN cc_start: 0.8018 (mt0) cc_final: 0.7732 (mt0) REVERT: B 60 GLU cc_start: 0.8324 (tp30) cc_final: 0.7932 (tt0) REVERT: B 87 LYS cc_start: 0.7998 (ttpp) cc_final: 0.7615 (ttmt) REVERT: b 165 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7684 (m110) REVERT: b 180 SER cc_start: 0.8875 (p) cc_final: 0.8552 (p) REVERT: b 429 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7561 (mtm110) REVERT: b 465 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7482 (tttm) REVERT: b 498 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7528 (mtpt) REVERT: C 31 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: C 77 LYS cc_start: 0.8123 (mttm) cc_final: 0.7552 (mmtt) REVERT: C 87 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7951 (ttpt) REVERT: c 202 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: c 297 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8069 (tp) REVERT: c 465 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7551 (tttm) REVERT: c 498 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7736 (mtpt) REVERT: D 46 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: D 105 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: F 46 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: F 69 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7829 (mtt) REVERT: G 89 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8595 (pt0) REVERT: H 46 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6497 (tm-30) outliers start: 75 outliers final: 58 residues processed: 223 average time/residue: 1.2229 time to fit residues: 302.7550 Evaluate side-chains 241 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 170 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 165 ASN Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 164 VAL Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 212 CYS Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 152 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** b 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 39 GLN G 38 GLN I 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16095 Z= 0.270 Angle : 0.517 10.859 21852 Z= 0.271 Chirality : 0.044 0.147 2574 Planarity : 0.004 0.048 2757 Dihedral : 5.146 54.309 2247 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.20 % Allowed : 15.75 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.85 (0.19), residues: 2016 helix: 2.49 (0.27), residues: 372 sheet: 0.58 (0.20), residues: 675 loop : -0.15 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 36 HIS 0.005 0.001 HIS a 317 PHE 0.011 0.001 PHE b 137 TYR 0.018 0.002 TYR c 457 ARG 0.003 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 170 time to evaluate : 1.765 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8288 (ttpp) cc_final: 0.7726 (ttmt) REVERT: a 202 GLN cc_start: 0.8022 (mt0) cc_final: 0.7728 (mt0) REVERT: B 87 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7631 (ttmt) REVERT: b 165 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7705 (m110) REVERT: b 180 SER cc_start: 0.8846 (p) cc_final: 0.8513 (p) REVERT: b 429 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7601 (mtp180) REVERT: b 465 LYS cc_start: 0.8210 (tmtt) cc_final: 0.7503 (tttm) REVERT: b 498 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7531 (mtpt) REVERT: C 31 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: C 77 LYS cc_start: 0.8115 (mttm) cc_final: 0.7569 (mmtt) REVERT: C 87 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7931 (ttpt) REVERT: c 202 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: c 297 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8084 (tp) REVERT: c 465 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7551 (tttm) REVERT: c 498 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7678 (mtpt) REVERT: D 46 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: D 105 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: E 89 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: F 46 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: F 69 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7827 (mtt) REVERT: G 89 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: H 46 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6502 (tm-30) outliers start: 76 outliers final: 58 residues processed: 224 average time/residue: 1.2477 time to fit residues: 309.3705 Evaluate side-chains 240 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 169 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 164 VAL Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 212 CYS Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN C 98 GLN F 39 GLN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16095 Z= 0.326 Angle : 0.551 11.242 21852 Z= 0.288 Chirality : 0.045 0.147 2574 Planarity : 0.004 0.048 2757 Dihedral : 5.284 54.566 2247 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.20 % Allowed : 15.81 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.72 (0.19), residues: 2016 helix: 2.37 (0.27), residues: 372 sheet: 0.55 (0.21), residues: 666 loop : -0.26 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 50 HIS 0.006 0.001 HIS a 317 PHE 0.012 0.001 PHE b 137 TYR 0.020 0.002 TYR c 457 ARG 0.004 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 171 time to evaluate : 1.794 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7716 (ttmt) REVERT: a 202 GLN cc_start: 0.7974 (mt0) cc_final: 0.7696 (mt0) REVERT: B 60 GLU cc_start: 0.8316 (tp30) cc_final: 0.7946 (tt0) REVERT: B 87 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7592 (ttmt) REVERT: b 165 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7755 (m110) REVERT: b 180 SER cc_start: 0.8866 (p) cc_final: 0.8541 (p) REVERT: b 272 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7218 (tttm) REVERT: b 429 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7573 (mtp180) REVERT: b 465 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7507 (tttm) REVERT: b 498 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7512 (mtpt) REVERT: C 77 LYS cc_start: 0.8089 (mttm) cc_final: 0.7519 (mmtt) REVERT: c 202 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7530 (mt0) REVERT: c 297 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8074 (tp) REVERT: c 396 MET cc_start: 0.9042 (ptp) cc_final: 0.8759 (ptm) REVERT: c 465 LYS cc_start: 0.8260 (tmtt) cc_final: 0.7541 (tttm) REVERT: c 498 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7654 (mtpt) REVERT: D 46 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: D 105 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: E 89 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: F 46 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: F 69 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7838 (mtt) REVERT: H 46 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6484 (tm-30) outliers start: 76 outliers final: 58 residues processed: 222 average time/residue: 1.2065 time to fit residues: 297.2711 Evaluate side-chains 241 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 171 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 272 LYS Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 481 LEU Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 164 VAL Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 159 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** b 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 39 GLN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16095 Z= 0.214 Angle : 0.494 11.361 21852 Z= 0.259 Chirality : 0.043 0.149 2574 Planarity : 0.004 0.049 2757 Dihedral : 5.061 54.095 2247 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.92 % Allowed : 16.31 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.86 (0.19), residues: 2016 helix: 2.57 (0.27), residues: 372 sheet: 0.60 (0.20), residues: 675 loop : -0.19 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 50 HIS 0.005 0.001 HIS a 317 PHE 0.009 0.001 PHE b 137 TYR 0.015 0.001 TYR a 457 ARG 0.002 0.000 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 174 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7711 (ttmt) REVERT: a 202 GLN cc_start: 0.8015 (mt0) cc_final: 0.7719 (mt0) REVERT: B 60 GLU cc_start: 0.8335 (tp30) cc_final: 0.7931 (tt0) REVERT: B 87 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7624 (ttmt) REVERT: b 165 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7697 (m110) REVERT: b 180 SER cc_start: 0.8827 (p) cc_final: 0.8510 (p) REVERT: b 272 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7193 (tttm) REVERT: b 429 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7594 (mtp180) REVERT: b 465 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7481 (tttm) REVERT: b 498 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7543 (mtpt) REVERT: C 77 LYS cc_start: 0.8108 (mttm) cc_final: 0.7555 (mmtt) REVERT: c 202 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: c 297 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8108 (tp) REVERT: c 429 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7600 (mtp180) REVERT: c 465 LYS cc_start: 0.8251 (tmtt) cc_final: 0.7536 (tttm) REVERT: c 498 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7741 (mtpt) REVERT: D 46 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6852 (tm-30) REVERT: D 105 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: E 89 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: F 46 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: F 69 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7829 (mtt) REVERT: H 46 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6470 (tm-30) outliers start: 71 outliers final: 57 residues processed: 225 average time/residue: 1.2142 time to fit residues: 304.0883 Evaluate side-chains 238 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 169 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain a residue 138 LEU Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 239 VAL Chi-restraints excluded: chain a residue 319 SER Chi-restraints excluded: chain a residue 335 THR Chi-restraints excluded: chain a residue 377 SER Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 442 VAL Chi-restraints excluded: chain a residue 498 LYS Chi-restraints excluded: chain a residue 501 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain b residue 165 ASN Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 239 VAL Chi-restraints excluded: chain b residue 272 LYS Chi-restraints excluded: chain b residue 319 SER Chi-restraints excluded: chain b residue 368 ASP Chi-restraints excluded: chain b residue 377 SER Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 410 LEU Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 498 LYS Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain c residue 190 SER Chi-restraints excluded: chain c residue 202 GLN Chi-restraints excluded: chain c residue 245 THR Chi-restraints excluded: chain c residue 266 ILE Chi-restraints excluded: chain c residue 297 LEU Chi-restraints excluded: chain c residue 319 SER Chi-restraints excluded: chain c residue 377 SER Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 498 LYS Chi-restraints excluded: chain c residue 501 GLN Chi-restraints excluded: chain c residue 503 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 159 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** b 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 39 GLN G 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130613 restraints weight = 16472.156| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.04 r_work: 0.3275 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16095 Z= 0.156 Angle : 0.463 11.416 21852 Z= 0.242 Chirality : 0.042 0.147 2574 Planarity : 0.003 0.050 2757 Dihedral : 4.873 53.944 2247 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.70 % Allowed : 16.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % 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: 0.99 (0.19), residues: 2016 helix: 2.77 (0.27), residues: 372 sheet: 0.69 (0.20), residues: 675 loop : -0.16 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.004 0.001 HIS a 317 PHE 0.007 0.001 PHE b 137 TYR 0.013 0.001 TYR a 457 ARG 0.002 0.000 ARG G 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5700.05 seconds wall clock time: 101 minutes 33.87 seconds (6093.87 seconds total)